diff --git a/R/process1KG.R b/R/process1KG.R index 7d653b43..7074a817 100644 --- a/R/process1KG.R +++ b/R/process1KG.R @@ -197,8 +197,8 @@ generateMapSnvSel <- function(cutOff=0.01, fileSNV, fileSNPsRDS, fileFREQ) { } ## Read the bulk SNP information file - mapSNVSel <- read.csv2(fileSNV) - + # mapSNVSel <- read.csv2(fileSNV) + mapSNVSel <- read.csv(fileSNV) ## Identify SNPs that have a frequency equal or superior to the cut-off ## in at least one super population listSNP <- which(rowSums(mapSNVSel[,c("EAS_AF", diff --git a/inst/extdata/matFreqSNV_Demo.txt.bz2 b/inst/extdata/matFreqSNV_Demo.txt.bz2 index c30dd4f8..11ed7d00 100644 Binary files a/inst/extdata/matFreqSNV_Demo.txt.bz2 and b/inst/extdata/matFreqSNV_Demo.txt.bz2 differ diff --git a/man/RAIDS-package.Rd b/man/RAIDS-package.Rd index 31215a20..d670a130 100644 --- a/man/RAIDS-package.Rd +++ b/man/RAIDS-package.Rd @@ -4,7 +4,6 @@ \encoding{UTF-8} \name{RAIDS-package} \alias{RAIDS-package} -\alias{_PACKAGE} \alias{RAIDS} \title{RAIDS: Accurate Inference of Genetic Ancestry from Cancer Sequences} \value{ diff --git a/tests/testthat/fixtures/matFreqSNV_Demo.txt.bz2 b/tests/testthat/fixtures/matFreqSNV_Demo.txt.bz2 index c30dd4f8..11ed7d00 100644 Binary files a/tests/testthat/fixtures/matFreqSNV_Demo.txt.bz2 and b/tests/testthat/fixtures/matFreqSNV_Demo.txt.bz2 differ diff --git a/tests/testthat/test-process1KG.R b/tests/testthat/test-process1KG.R index 62a2b917..4479bf38 100644 --- a/tests/testthat/test-process1KG.R +++ b/tests/testthat/test-process1KG.R @@ -173,18 +173,18 @@ test_that("generateMapSnvSel() must generate expected output", { 54489, 54707, 54715), REF=c("T", "T", "C", "G", "G", "G", "C"), ALT=c("G", "A", "A", "A", "A", "C", "T"), - AF=as.character(c(0.02, 0.11, 0.08, 0.07, - 0.1, 0.23, 0.21)), - EAS_AF=c("0.0", "0.0", "0.05", "0.01", - "0.0", "0.08", "0.07"), - EUR_AF=c("0.04", "0.2", "0.12", "0.14", - "0.18", "0.38", "0.34"), - AFR_AF=c("0.03", "0.02", "0.05", "0.06", - "0.02", "0.18", "0.16"), - AMR_AF=c("0.03", "0.12", "0.06", "0.07", - "0.1", "0.25", "0.24"), - SAS_AF=c("0.02", "0.22", "0.1", "0.09", - "0.21", "0.28", "0.27"), + AF=c(0.02, 0.11, 0.08, 0.07, + 0.1, 0.23, 0.21), + EAS_AF=c(0.0, 0.0, 0.05, 0.01, + 0.0, 0.08, 0.07), + EUR_AF=c(0.04, 0.2, 0.12, 0.14, + 0.18, 0.38, 0.34), + AFR_AF=c(0.03, 0.02, 0.05, 0.06, + 0.02, 0.18, 0.16), + AMR_AF=c(0.03, 0.12, 0.06, 0.07, + 0.1, 0.25, 0.24), + SAS_AF=c(0.02, 0.22, 0.1, 0.09, + 0.21, 0.28, 0.27), stringsAsFactors = FALSE) expect_equivalent(readRDS(filterSNVFile), snpFilteredExpected)