R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> suppressPackageStartupMessages(library(GGtools))
> 
> # configure
>    cc = new("CisConfig")
>    chrnames(cc) = "21"
>    genome(cc) = "hg19"
>    nperm(cc) = 2L
>    lkp = try(library(parallel))
>    if (!inherits(lkp, "try-error")) {
+       nc = min(10, detectCores())
+       options(mc.cores=nc)
+       geneApply(cc) = mclapply
+       }
>    estimates(cc) = FALSE
>    set.seed(1234)
> #   system.time(f1 <- cisScores( cc ))
>  #
>  # demonstrate adding annotation on chromatin state and gwas status
>  #
>  eprops = function(ans) {
+  #
+  # only adds fields to values() of the input
+  #
+   data(hmm878)
+   ac = as.character
+   eqr = GRanges(ac(seqnames(ans)), IRanges(ans$snplocs, width=1))
+   fo = findOverlaps(eqr, hmm878)
+   chromcat878 = factor(rep("none", length(ans)), levels=c(unique(hmm878$name), "none"))
+   chromcat878[ queryHits(fo) ] = factor(hmm878$name[subjectHits(fo)])
+   ans$chromcat878 = chromcat878
+  
+   if (require(gwascat)) {
+     data(gwastagger)
+     isgwashit = 1*(overlapsAny(eqr, gwastagger) | ans$snp %in% gwastagger$tagid) # allow match by loc or name
+     ans$isgwashit = isgwashit
+     }
+   ans
+  }
>  extraProps(cc) = eprops
>  set.seed(1234)
>  rhs(cc) = ~1-1
> if (.Platform$OS.type != "windows") {
+  (f2 <- cisScores( cc ))
+  isTRUE(sum(f2$fdr < 0.05) == 172)  # can change with annotation or location changes, check serialized results if necessary
+ }
> TRUE
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  18.14    1.54   19.67 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> suppressPackageStartupMessages(library(GGtools))
> 
> # configure
>    cc = new("CisConfig")
>    chrnames(cc) = "21"
>    genome(cc) = "hg19"
>    nperm(cc) = 2L
>    lkp = try(library(parallel))
>    if (!inherits(lkp, "try-error")) {
+       nc = min(10, detectCores())
+       options(mc.cores=nc)
+       geneApply(cc) = mclapply
+       }
>    estimates(cc) = FALSE
>    set.seed(1234)
> #   system.time(f1 <- cisScores( cc ))
>  #
>  # demonstrate adding annotation on chromatin state and gwas status
>  #
>  eprops = function(ans) {
+  #
+  # only adds fields to values() of the input
+  #
+   data(hmm878)
+   ac = as.character
+   eqr = GRanges(ac(seqnames(ans)), IRanges(ans$snplocs, width=1))
+   fo = findOverlaps(eqr, hmm878)
+   chromcat878 = factor(rep("none", length(ans)), levels=c(unique(hmm878$name), "none"))
+   chromcat878[ queryHits(fo) ] = factor(hmm878$name[subjectHits(fo)])
+   ans$chromcat878 = chromcat878
+  
+   if (require(gwascat)) {
+     data(gwastagger)
+     isgwashit = 1*(overlapsAny(eqr, gwastagger) | ans$snp %in% gwastagger$tagid) # allow match by loc or name
+     ans$isgwashit = isgwashit
+     }
+   ans
+  }
>  extraProps(cc) = eprops
>  set.seed(1234)
>  rhs(cc) = ~1-1
> if (.Platform$OS.type != "windows") {
+  (f2 <- cisScores( cc ))
+  isTRUE(sum(f2$fdr < 0.05) == 172)  # can change with annotation or location changes, check serialized results if necessary
+ }
> TRUE
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  16.95    0.84   17.78 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> # april 2011/jan 2012
> # compares gwSnpTests to eqtlTests
> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:Matrix':

    which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> hmceuB36.2021 <- getSS("GGtools", c("20"))
> library(illuminaHumanv1.db)

> cp = get("CPNE1", revmap(illuminaHumanv1SYMBOL))
> hcp = hmceuB36.2021[ probeId(cp), ]
> t1 = gwSnpTests(genesym("CPNE1")~male, hcp)
> pick = as([email protected][[1]], "data.frame")[22101:22115,]
> rsids = rownames(pick)[!is.na(pick[,1])]
> csq = pick[rsids,1]
> names(csq) = rsids
> fi = tempfile()
> if (file.exists(fi)) unlink(fi, recursive=TRUE)
> t2 = eqtlTests(hcp, ~male, targdir=fi)
> sco = t2[rsids,][,1]
> unlink(fi, recursive=TRUE)
> comp = (sco-trunc(100*csq,0)/100)/sco
> (!(max(abs(comp)) > .01))
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
  25.20    2.71   27.92 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> # april 2011/jan 2012
> # compares gwSnpTests to eqtlTests
> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:Matrix':

    which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> hmceuB36.2021 <- getSS("GGtools", c("20"))
> library(illuminaHumanv1.db)

> cp = get("CPNE1", revmap(illuminaHumanv1SYMBOL))
> hcp = hmceuB36.2021[ probeId(cp), ]
> t1 = gwSnpTests(genesym("CPNE1")~male, hcp)
> pick = as([email protected][[1]], "data.frame")[22101:22115,]
> rsids = rownames(pick)[!is.na(pick[,1])]
> csq = pick[rsids,1]
> names(csq) = rsids
> fi = tempfile()
> if (file.exists(fi)) unlink(fi, recursive=TRUE)
> t2 = eqtlTests(hcp, ~male, targdir=fi)
> sco = t2[rsids,][,1]
> unlink(fi, recursive=TRUE)
> comp = (sco-trunc(100*csq,0)/100)/sco
> (!(max(abs(comp)) > .01))
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
  25.59    1.82   28.37 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:Matrix':

    which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> library(ff)
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:data.table':

    setattr

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp2XF2Ph"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==37570478.08 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

> 
> tenOn2021 =
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S")
> 
> c22 = getSS("GGdata", "22")
> c22 = c22[probeId(tenOn2021),]
> 
> e1 = eqtlTests(c22, ~1, targdir = "ooo")
> m1 = meqtlTests(list(c22, c22), list(~1, ~1), targdir = "ooobb")
> 
> ae = as.ram(e1@fffile)
opening ff C:/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests_i386/ooo/foo_chr22.ff
> am = as.ram(m1@fffile)
> all.equal(as.numeric(ae)*2 ,as.numeric(am) )
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
  25.23    2.39   33.70 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:Matrix':

    which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

The following object is masked from 'package:grDevices':

    windows

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> library(ff)
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:data.table':

    setattr

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0q9pCf"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==685831618.56 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

> 
> tenOn2021 =
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S")
> 
> c22 = getSS("GGdata", "22")
> c22 = c22[probeId(tenOn2021),]
> 
> e1 = eqtlTests(c22, ~1, targdir = "ooo")
> m1 = meqtlTests(list(c22, c22), list(~1, ~1), targdir = "ooobb")
> 
> ae = as.ram(e1@fffile)
opening ff C:/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests_x64/ooo/foo_chr22.ff
> am = as.ram(m1@fffile)
> all.equal(as.numeric(ae)*2 ,as.numeric(am) )
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
  33.73    2.04   35.78 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> heavyTest = function() {
+ library(GGtools)
+ 
+ # verifies that transScores agrees with snp.rhs.tests to obtain best
+ # trans scores
+ 
+ tenOn2021 = 
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") 
+ 
+ suppressPackageStartupMessages(library(GGtools))
+ 
+ mt1 = meta.transScores(c("GGdata", "GGdata"), rhs=list(~1, ~1), snpchr="22", chrnames=as.character(c(20,21)),
+ #
+ # all tests are trans, to verify buffering approach
+ #
+         radius = 2e+06,  K=4, targdir="uiu2",
+     probesToKeep = tenOn2021, batchsize = 200, 
+     geneannopk = "illuminaHumanv1.db", 
+     snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", SMFilterList = list( function(x) x[probeId(tenOn2021),],
+          function(x) x[probeId(tenOn2021), ]),
+     schrpref = "ch", exFilter = list( function(x) x, function(x) x)) 
+ 
+ transTab(mt1)
+ }
> 
> proc.time()
   user  system elapsed 
   0.20    0.06    0.25 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> heavyTest = function() {
+ library(GGtools)
+ 
+ # verifies that transScores agrees with snp.rhs.tests to obtain best
+ # trans scores
+ 
+ tenOn2021 = 
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") 
+ 
+ suppressPackageStartupMessages(library(GGtools))
+ 
+ mt1 = meta.transScores(c("GGdata", "GGdata"), rhs=list(~1, ~1), snpchr="22", chrnames=as.character(c(20,21)),
+ #
+ # all tests are trans, to verify buffering approach
+ #
+         radius = 2e+06,  K=4, targdir="uiu2",
+     probesToKeep = tenOn2021, batchsize = 200, 
+     geneannopk = "illuminaHumanv1.db", 
+     snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", SMFilterList = list( function(x) x[probeId(tenOn2021),],
+          function(x) x[probeId(tenOn2021), ]),
+     schrpref = "ch", exFilter = list( function(x) x, function(x) x)) 
+ 
+ transTab(mt1)
+ }
> 
> proc.time()
   user  system elapsed 
   0.25    0.07    0.31 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (.Platform$OS.type != "windows") {
+ t20 = GGtools:::getCisMap()
+ 
+ NL = GGtools:::namelist(t20)
+ 
+ NL1 = NL[[1]]
+ 
+ t20sl = t20@snplocs[NL1]
+ 
+ probe1 = names(NL)[1]
+ 
+ TARG = t20@generanges[probe1]-50000
+ 
+ d = distance(TARG, t20sl)
+ 
+ all(d <= 50000)
+ } else TRUE
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   0.23    0.03    0.25 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (.Platform$OS.type != "windows") {
+ t20 = GGtools:::getCisMap()
+ 
+ NL = GGtools:::namelist(t20)
+ 
+ NL1 = NL[[1]]
+ 
+ t20sl = t20@snplocs[NL1]
+ 
+ probe1 = names(NL)[1]
+ 
+ TARG = t20@generanges[probe1]-50000
+ 
+ d = distance(TARG, t20sl)
+ 
+ all(d <= 50000)
+ } else TRUE
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   0.26    0.04    0.29 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # verifies that transScores agrees with snp.rhs.tests to obtain best
> # trans scores
> 
> suppressPackageStartupMessages(library(GGtools))
> 
> tenOn2021 = 
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") 
> 
> tconf = new("TransConfig")
> radius(tconf) = 2000000L
> smpack(tconf) = "GGdata"
> rhs(tconf) = ~1
> snpchr(tconf) = "22"  # we get scores for all SNP on this chrom
> chrnames(tconf) = c("20", "21")
> gbufsize(tconf) = 4L
> smFilter(tconf) = function(x) x[probeId(tenOn2021),]
> snpannopk(tconf) = snplocsDefault()
> schrpref(tconf) = "ch"
> exFilter(tconf) = function(x)x
> gchrpref = ""
> batchsize(tconf) = 200L
> 
> suppressPackageStartupMessages(library(GGtools))
> 
> t1 = transScores(tconf)
Loading required package: illuminaHumanv1.db

opening ff C:/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsc_20_chr22.ff
2opening ff C:/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests_i386/cisScratch22/tsctmp2_chr22.ff
> 
> #"GGdata", rhs=~1, snpchr="22", chrnames=as.character(c(20,21)),
> #
> # all tests are trans, to verify buffering approach
> #
> #        radius = 2e+06,  K=4,
> #    probesToKeep = tenOn2021, batchsize = 200, 
> #    geneannopk = "illuminaHumanv1.db", 
> #    snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", 
> #    schrpref = "ch", exFilter = function(x) x) 
> 
> if (.Platform$OS.type != "windows") {
+   tt1 = transTab(t1)
+   
+   cleanup_transff = function(x) {
+    fn = attr(attr(x@base$scores, "physical"), "filename")
+    comps = strsplit(fn, "/")[[1]]
+    nel = length(comps)
+    unlink(comps[nel-1], recursive=TRUE)
+   }
+   
+   cleanup_transff(t1)
+   
+   c22 = getSS("GGdata", "22")
+   
+   exl = lapply(tenOn2021, function(x) exprs(c22)[x,])
+   rhst = lapply(1:length(exl), function(g) {
+        ex = exl[[g]]
+        snp.rhs.tests(ex~1, snp.data=smList(c22)[[1]], fam="gaussian", uncertain=TRUE) })
+   csnp1 = sapply(rhst, function(x)chi.squared(x)[1])
+   csnp50 = sapply(rhst, function(x)chi.squared(x)[50])
+   
+   
+   #all(abs(floor(sort(csnp1, decreasing=TRUE)[1:4]*10)/10 - tt1[1:4,2]) < .01)
+   #all(abs(floor(sort(csnp50, decreasing=TRUE)[1:4]*10)/10 - tt1[197:200,2]) < 0.01)
+   
+   ttdt = data.table(tt1)
+   SS = sort(sapply(rhst, function(x) max(chi.squared(x), na.rm=TRUE))) 
+   TT = sort(ttdt[,max(chisq),by="probeid"]$V1) 
+   maxchk = (max(abs(SS-TT))<.01)
+   
+   # needs more work, tt1 is organized by snp
+   #SS = sort(sapply(rhst, function(x) min(chi.squared(x), na.rm=TRUE))) 
+   #TT = sort(ttdt[,min(chisq),by="probeid"]$V1) 
+   #minchk = (max(abs(SS-TT))<.01)
+   
+   maxchk 
+ }
>   
> 
> proc.time()
   user  system elapsed 
  63.89    7.65   75.50 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # verifies that transScores agrees with snp.rhs.tests to obtain best
> # trans scores
> 
> suppressPackageStartupMessages(library(GGtools))
> 
> tenOn2021 = 
+ c( "GI_4557248-S",  "GI_15451784-S", "GI_4557678-S", "GI_9951914-S", "GI_21327679-S",
+  "GI_7669476-I", "GI_7669478-A", "GI_4557290-I", "GI_4557294-A", "GI_41406053-S") 
> 
> tconf = new("TransConfig")
> radius(tconf) = 2000000L
> smpack(tconf) = "GGdata"
> rhs(tconf) = ~1
> snpchr(tconf) = "22"  # we get scores for all SNP on this chrom
> chrnames(tconf) = c("20", "21")
> gbufsize(tconf) = 4L
> smFilter(tconf) = function(x) x[probeId(tenOn2021),]
> snpannopk(tconf) = snplocsDefault()
> schrpref(tconf) = "ch"
> exFilter(tconf) = function(x)x
> gchrpref = ""
> batchsize(tconf) = 200L
> 
> suppressPackageStartupMessages(library(GGtools))
> 
> t1 = transScores(tconf)
Loading required package: illuminaHumanv1.db

opening ff C:/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests_x64/cisScratch22/tsc_20_chr22.ff
2opening ff C:/Users/biocbuild/bbs-3.9-bioc/meat/GGtools.Rcheck/tests_x64/cisScratch22/tsctmp2_chr22.ff
> 
> #"GGdata", rhs=~1, snpchr="22", chrnames=as.character(c(20,21)),
> #
> # all tests are trans, to verify buffering approach
> #
> #        radius = 2e+06,  K=4,
> #    probesToKeep = tenOn2021, batchsize = 200, 
> #    geneannopk = "illuminaHumanv1.db", 
> #    snpannopk = "SNPlocs.Hsapiens.dbSNP.20111119", gchrpref = "", 
> #    schrpref = "ch", exFilter = function(x) x) 
> 
> if (.Platform$OS.type != "windows") {
+   tt1 = transTab(t1)
+   
+   cleanup_transff = function(x) {
+    fn = attr(attr(x@base$scores, "physical"), "filename")
+    comps = strsplit(fn, "/")[[1]]
+    nel = length(comps)
+    unlink(comps[nel-1], recursive=TRUE)
+   }
+   
+   cleanup_transff(t1)
+   
+   c22 = getSS("GGdata", "22")
+   
+   exl = lapply(tenOn2021, function(x) exprs(c22)[x,])
+   rhst = lapply(1:length(exl), function(g) {
+        ex = exl[[g]]
+        snp.rhs.tests(ex~1, snp.data=smList(c22)[[1]], fam="gaussian", uncertain=TRUE) })
+   csnp1 = sapply(rhst, function(x)chi.squared(x)[1])
+   csnp50 = sapply(rhst, function(x)chi.squared(x)[50])
+   
+   
+   #all(abs(floor(sort(csnp1, decreasing=TRUE)[1:4]*10)/10 - tt1[1:4,2]) < .01)
+   #all(abs(floor(sort(csnp50, decreasing=TRUE)[1:4]*10)/10 - tt1[197:200,2]) < 0.01)
+   
+   ttdt = data.table(tt1)
+   SS = sort(sapply(rhst, function(x) max(chi.squared(x), na.rm=TRUE))) 
+   TT = sort(ttdt[,max(chisq),by="probeid"]$V1) 
+   maxchk = (max(abs(SS-TT))<.01)
+   
+   # needs more work, tt1 is organized by snp
+   #SS = sort(sapply(rhst, function(x) min(chi.squared(x), na.rm=TRUE))) 
+   #TT = sort(ttdt[,min(chisq),by="probeid"]$V1) 
+   #minchk = (max(abs(SS-TT))<.01)
+   
+   maxchk 
+ }
>   
> 
> proc.time()
   user  system elapsed 
  88.57    2.31  101.76