R/sscore2.R
In mfmiles/Sscore2: Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
Defines functions
sscore2
sscore2 <- function(celFile1 = NULL, celFile2 = NULL, celTable = NULL, celTab.names = FALSE, typeFilter = 1, method = 1, SF1 = NULL, SF2 = NULL, fileout = FALSE, gzip = FALSE, verbose = FALSE) {
# Insert fake-NULL fix to prevent 'no visible binding for global variable' in R CMD check:
fs1_man_fsetid <- transcript_cluster_id <- probeset_id <- transcriptClusterID <- category <- probesetType <- transcriptID <- '.' <- geneName <- probe_type <- probesetID <- NULL
# suppress warnings in functin due to 'closing unsed connection' warning for ReadCel()
# as used within the sscore2() function:
# options(warn = -1)
if (is.null(celTable)) stopifnot(!is.null(celFile1), !is.null(celFile2))
else if (is.null(celFile1) & is.null(celFile2)) stopifnot(!is.null(celTable))
else stop("INPUT EITHER CELFILES OR CELTABLE")
# DEFINE CHIP-TYPES THAT THE SSCORE2 CODE IS COMPATIABLE WITH
chip430 <- c("Rhesus", "Mouse430_2")
chipGene <- c("MoGene-2_1-st", "MoGene-1_0-st-v1", "DroGene-1_0-st")
chipTrans <- c("MTA-1_0", "Clariom_S_Mouse")
chipType <- c(chip430, chipGene, chipTrans)
if (!is.null(celTable)) {
if (!is.data.table(celTable)) celTable <- as.data.table(celTable)
chipType1 <- chipType2 <- vector("character", length = nrow(celTable))
for (i in 1:nrow(celTable)) {
stopifnot (!is.null(celTable[[2]][i]), !is.null(celTable[[3]][i]))
chipType1[i] <- readCelHeader(celTable[[2]][i])$chiptype
chipType2[i] <- readCelHeader(celTable[[3]][i])$chiptype
}
if (all.equal(chipType1, chipType2)) chip <- chipType1[1]
} else if (!is.null(celFile1) & !is.null(celFile2)) {
celHead1 <- readCelHeader(celFile1)
celHead2 <- readCelHeader(celFile2)
# closeAllConnections()
# gc()
if (identical(celHead1$chiptype, celHead2$chiptype)) assign("chip", celHead1$chiptype)
}
if (chip %in% chipType) {
# packageName <- paste(chipType, "data.gz", sep = "")
# while (!require(packageName)) biocLite(packageName)
print("READING PROBE FILE")
if (chip == "Clariom_S_Mouse") {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomS_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))}
else if (chip == "MTA-1_0" & method == 1) {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomD_geneCDF_probefile.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: MTA gene-level PROBE FILE")}
else if (chip == "MTA-1_0" & method == 2) {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomD_exonCDF_probefile.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: MTA exon-level PROBE FILE")}
else if (chip == "MTA-1_0" & method == 3) {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomD_to_S_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: ClariomD_to_S PROBE FILE")}
else if (chip == "Mouse430_2") {probeFile <- fread(gunzip(system.file("extdata","Mouse_430_2_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: Mouse430_2 PROBE FILE")}
else if (chip == "MoGene-1_0-st-v1") {probeFile <- fread(gunzip(system.file("extdata","Mouse_Gene_1_0ST_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: MoGene-1_0-st PROBE FILE")}
}
while (method != 1 & method != 2 & method != 3 & method != 4) method <- as.numeric(readline("ENTER METHOD BASED ON 'chipType': "))
if (!(chip %chin% chip430)) {
trim <- 0.04
if (chip == "MTA-1_0" & method == 1) {
bgp_list <- fread(gunzip(system.file("extdata","Mouse_ClariomD_bgp_probelist.csv.gz",package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
bgp <- probeFile[fs1_man_fsetid %in% bgp_list$probesets_bgp]}
else if (chip == "MTA-1_0" & method == 2) {
bgp <- probeFile[fs1_man_fsetid %like% "AFFX-BkGr-GC"]}
else if (chip == "MTA-1_0" & method == 3) {
bgp <- probeFile[transcriptClusterID %like% "AFFX-BkGr-GC"]}
else if (chip == "MoGene-1_0-st-v1" & method == 1) {
bgp <- probeFile[category %chin% "control->bgp->antigenomic"]}
else bgp <- probeFile[probesetType %chin% "control->bgp->antigenomic"]
while (typeFilter != 0 & typeFilter != 1) typeFilter <- as.numeric(readline("USE ALL PROBES (0) OR MAIN PROBES (1) FOR S-SCORE CALCULATION: "))
if (chip %chin% chipTrans) {
if (typeFilter == 0) print("USING ALL PROBES FOR S-SCORE CALCULATION")
else if (method == 1 & chip == "MTA-1_0") {
# print("USING ALL MAIN PSRS PROBES FOR S-SCORE CALCULATION")
print("USING ALL 'MTA gene-level CDF' probes FOR S-SCORE CALCULATION")
# probeFile <- probeFile[probesetType %chin% "main->psrs"]
} else if (method == 2 & chip == "MTA-1_0") {
print("USING ALL 'MTA exon-level CDF' probes FOR S-SCORE CALCULATION")
}
else if (typeFilter == 0 & chip == "Clariom_S_Mouse") {
print("USING ALL PROBES FOR S-SCORE CALCULATION")
}
else if (typeFilter == 1 & chip == "Clariom_S_Mouse") {
probeFile <- probeFile[category %chin% "main"]
print("USING ONLY MAIN-TC PROBES FOR S-SCORE CALCULATION")
}
} else if (chip %chin% chipGene) {
if (typeFilter == 0) print("USING ALL PROBES FOR S-SCORE CALCULATION")
else if (typeFilter == 1) {
print("USING ALL MAIN PROBES FOR S-SCORE CALCULATION")
probeFile <- probeFile[category %chin% "main"]
}
} else print("'typeFilter' NOT APPLIED")
if (method == 1) {
if (chip == "MTA-1_0") {
methodTag <- "geneCDF"
method <- "fs1_man_fsetid"
}
else if (chip == "Clariom_S_Mouse") {
methodTag <- "TCid"
method <- c("transcriptClusterID", "probeset_list", "geneName", "locus_type", "probesetType", "chr_num", "chr_start", "chr_stop", "chr_strand")
# method <- "transcriptClusterID"
}
else if (chip == "MoGene-1_0-st-v1") {
methodTag <- "TCid"
method <- "transcriptClusterID"
}
info <- probeFile[,.(nProbes = .N), keyby = method]
# Use 'nProbes' to check against 'total_probes' from 'MTA_annot_TCid' from affy
}
else if (method == 2 & chip == "MTA-1_0") {
methodTag <- "exonCDF"
method <- "fs1_man_fsetid"
info <- probeFile[,.(nProbes = .N), keyby = method]
}
else if (method == 3 & chip == "MTA-1_0") {
methodTag <- "D_to_S"
probeFile <- probeFile[!geneName %chin% ""]
method <- "transcriptClusterID"
mergeKey = c(method, "probeID")
info <- probeFile[,.N, keyby = mergeKey][,.(nProbes = .N), keyby = method]
} else stop("NO METHOD APPLIED")
if (!identical(key(info), method)) setkeyv(info, method)
} else if (chip %in% chip430) {
trim <- 0.02
# bgp <- probeFile[probeType %chin% "misMatch"]
bgp <- probeFile[probe_type %chin% "mm"]
# probeFile <- probeFile[probeType %chin% "perfectMatch"]
probeFile <- probeFile[probe_type %chin% "pm"]
if (method == 1) method <- methodTag <- "pmmm"
else if (method == 2) method <- methodTag <- "gc"
# info <- probeFile[,.N, keyby = .(probesetID, probesetName)]
info <- probeFile[,.N, keyby = .(probesetID)]
} else stop("CHIP TYPE NOT FOUND")
if (!identical(key(probeFile), key(info))) {
setkeyv(probeFile, key(info))
setkeyv(bgp, key(info))
# setkey(bgp, probeset_id)
}
cIdx <- length(colnames(info))
infoKey <- key(info)
if (is.character(method)) {
if (!is.null(celTable)) {
for (i in 1:nrow(celTable)) {
print("READING CEL FILES")
cel1 <- readCel(celTable[[2]][i], readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
cel2 <- readCel(celTable[[3]][i], readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
Score <- computeSscore(cel1, cel2, probeFile, bgp, method, SF1 = SF1, SF2 = SF2, verbose = verbose, trim = trim)
info <- info[Score, on = infoKey]
if (celTab.names){
print("Custom run name for BATCH job:")
colnames(info)[cIdx + i] <- as.character(celTable[i,1])
print(as.character(celTable[i,1]))
}
else{
print("Standard run name for BATCH job:")
#colnames(info)[cIdx + i] <- paste("RUN_", i, sep = "")
# Add filenames to colname (CEL_1 vs CEL_2)
celName1 <- strsplit(cel1$header$filename, "/")[[1]]; celName1 <- celName1[length(celName1)]
celName2 <- strsplit(cel2$header$filename, "/")[[1]]; celName2 <- celName2[length(celName2)]
colnames(info)[cIdx + i] <- paste(celName1, "vs", celName2)
print(paste(celName1, "vs", celName2))
}
}
} else if (!is.null(celFile1) & !is.null(celFile2)) {
print("READING CEL FILES")
cel1 <- readCel(celFile1, readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
cel2 <- readCel(celFile2, readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
Score <- computeSscore(cel1, cel2, probeFile, bgp, method, SF1 = SF1, SF2 = SF2, verbose = verbose, trim = trim)
info <- info[Score, on = infoKey]
colnames(info)[cIdx + 1] <- "Sscore"
# Add filenames to colname (CEL_1 vs CEL_2):
# celName1 <- strsplit(cel1$header$filename, "/")[[1]]; celName1 <- celName1[length(celName1)]
# celName2 <- strsplit(cel2$header$filename, "/")[[1]]; celName2 <- celName2[length(celName2)]
# colnames(info)[cIdx + 1] <- paste(celName1, "vs", celName2)
# print("Sscore2 run output assigned to column name:")
# print(paste(celName1, "vs", celName2))
}
# if (verbose) View (info)
}
# Add annotations to ClariomD/MTA arrays:
if (methodTag == "geneCDF" & chip == "MTA-1_0"){
print("Adding gene-level annotations to MTA/ClariomD Sscores")
annot <- fread(gunzip(system.file("extdata","Mouse_ClariomD_TCid_geneCDF_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
setkey(annot,transcript_cluster_id)
info <- annot[info]
info <- info[transcript_cluster_id %like% ".mm.1"]
info <- info[,probeset_id := NULL]
}
if (methodTag == "exonCDF" & chip == "MTA-1_0"){
print("Adding exon-level annotations to MTA/ClariomD Ssscores")
annot <- fread(gunzip(system.file("extdata","Mouse_ClariomD_PSR_exonCDF_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
setkey(annot,probeset_id)
info <- annot[info]
info <- info[probeset_id %like% ".mm.1"]
# info <- annot[transcript_cluster_id %like% ".mm.1"]
}
if (methodTag == "D_to_S" & chip == "MTA-1_0"){
print("Adding gene-level annotations for to ClariomD-masked-to-ClariomS Sscores")
annot <- fread(gunzip(system.file("extdata","Mouse_ClariomS_affyyannot_na36.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
setkey(annot,transcript_cluster_id)
info <- annot[info]
}
if (fileout) {
#ID tag: a custom formatted timestamp applied to all written files
ID <- format(Sys.time(), "%Y%m%d_%H%M%S")
fileName <- paste(chip, "_", methodTag, "_", "Sscore2_", ID, ".csv", sep = "")
print("WRITING S-SCORE OUTPUT TO DIRECTORY")
fwrite(info, fileName)
}
if (gzip) {
print("COMPRESSING SSCORE OUTPUT FILE")
system(paste("gzip", fileName))
}
print("DONE")
# options(warn = 0)
return(info)
}
mfmiles/Sscore2 documentation built on Oct. 1, 2019, 6:04 a.m.
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Defines functions sscore2
sscore2 <- function(celFile1 = NULL, celFile2 = NULL, celTable = NULL, celTab.names = FALSE, typeFilter = 1, method = 1, SF1 = NULL, SF2 = NULL, fileout = FALSE, gzip = FALSE, verbose = FALSE) {
# Insert fake-NULL fix to prevent 'no visible binding for global variable' in R CMD check:
fs1_man_fsetid <- transcript_cluster_id <- probeset_id <- transcriptClusterID <- category <- probesetType <- transcriptID <- '.' <- geneName <- probe_type <- probesetID <- NULL
# suppress warnings in functin due to 'closing unsed connection' warning for ReadCel()
# as used within the sscore2() function:
# options(warn = -1)
if (is.null(celTable)) stopifnot(!is.null(celFile1), !is.null(celFile2))
else if (is.null(celFile1) & is.null(celFile2)) stopifnot(!is.null(celTable))
else stop("INPUT EITHER CELFILES OR CELTABLE")
# DEFINE CHIP-TYPES THAT THE SSCORE2 CODE IS COMPATIABLE WITH
chip430 <- c("Rhesus", "Mouse430_2")
chipGene <- c("MoGene-2_1-st", "MoGene-1_0-st-v1", "DroGene-1_0-st")
chipTrans <- c("MTA-1_0", "Clariom_S_Mouse")
chipType <- c(chip430, chipGene, chipTrans)
if (!is.null(celTable)) {
if (!is.data.table(celTable)) celTable <- as.data.table(celTable)
chipType1 <- chipType2 <- vector("character", length = nrow(celTable))
for (i in 1:nrow(celTable)) {
stopifnot (!is.null(celTable[[2]][i]), !is.null(celTable[[3]][i]))
chipType1[i] <- readCelHeader(celTable[[2]][i])$chiptype
chipType2[i] <- readCelHeader(celTable[[3]][i])$chiptype
}
if (all.equal(chipType1, chipType2)) chip <- chipType1[1]
} else if (!is.null(celFile1) & !is.null(celFile2)) {
celHead1 <- readCelHeader(celFile1)
celHead2 <- readCelHeader(celFile2)
# closeAllConnections()
# gc()
if (identical(celHead1$chiptype, celHead2$chiptype)) assign("chip", celHead1$chiptype)
}
if (chip %in% chipType) {
# packageName <- paste(chipType, "data.gz", sep = "")
# while (!require(packageName)) biocLite(packageName)
print("READING PROBE FILE")
if (chip == "Clariom_S_Mouse") {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomS_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))}
else if (chip == "MTA-1_0" & method == 1) {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomD_geneCDF_probefile.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: MTA gene-level PROBE FILE")}
else if (chip == "MTA-1_0" & method == 2) {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomD_exonCDF_probefile.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: MTA exon-level PROBE FILE")}
else if (chip == "MTA-1_0" & method == 3) {probeFile <- fread(gunzip(system.file("extdata","Mouse_ClariomD_to_S_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: ClariomD_to_S PROBE FILE")}
else if (chip == "Mouse430_2") {probeFile <- fread(gunzip(system.file("extdata","Mouse_430_2_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: Mouse430_2 PROBE FILE")}
else if (chip == "MoGene-1_0-st-v1") {probeFile <- fread(gunzip(system.file("extdata","Mouse_Gene_1_0ST_probefile_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
print("READ IN: MoGene-1_0-st PROBE FILE")}
}
while (method != 1 & method != 2 & method != 3 & method != 4) method <- as.numeric(readline("ENTER METHOD BASED ON 'chipType': "))
if (!(chip %chin% chip430)) {
trim <- 0.04
if (chip == "MTA-1_0" & method == 1) {
bgp_list <- fread(gunzip(system.file("extdata","Mouse_ClariomD_bgp_probelist.csv.gz",package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
bgp <- probeFile[fs1_man_fsetid %in% bgp_list$probesets_bgp]}
else if (chip == "MTA-1_0" & method == 2) {
bgp <- probeFile[fs1_man_fsetid %like% "AFFX-BkGr-GC"]}
else if (chip == "MTA-1_0" & method == 3) {
bgp <- probeFile[transcriptClusterID %like% "AFFX-BkGr-GC"]}
else if (chip == "MoGene-1_0-st-v1" & method == 1) {
bgp <- probeFile[category %chin% "control->bgp->antigenomic"]}
else bgp <- probeFile[probesetType %chin% "control->bgp->antigenomic"]
while (typeFilter != 0 & typeFilter != 1) typeFilter <- as.numeric(readline("USE ALL PROBES (0) OR MAIN PROBES (1) FOR S-SCORE CALCULATION: "))
if (chip %chin% chipTrans) {
if (typeFilter == 0) print("USING ALL PROBES FOR S-SCORE CALCULATION")
else if (method == 1 & chip == "MTA-1_0") {
# print("USING ALL MAIN PSRS PROBES FOR S-SCORE CALCULATION")
print("USING ALL 'MTA gene-level CDF' probes FOR S-SCORE CALCULATION")
# probeFile <- probeFile[probesetType %chin% "main->psrs"]
} else if (method == 2 & chip == "MTA-1_0") {
print("USING ALL 'MTA exon-level CDF' probes FOR S-SCORE CALCULATION")
}
else if (typeFilter == 0 & chip == "Clariom_S_Mouse") {
print("USING ALL PROBES FOR S-SCORE CALCULATION")
}
else if (typeFilter == 1 & chip == "Clariom_S_Mouse") {
probeFile <- probeFile[category %chin% "main"]
print("USING ONLY MAIN-TC PROBES FOR S-SCORE CALCULATION")
}
} else if (chip %chin% chipGene) {
if (typeFilter == 0) print("USING ALL PROBES FOR S-SCORE CALCULATION")
else if (typeFilter == 1) {
print("USING ALL MAIN PROBES FOR S-SCORE CALCULATION")
probeFile <- probeFile[category %chin% "main"]
}
} else print("'typeFilter' NOT APPLIED")
if (method == 1) {
if (chip == "MTA-1_0") {
methodTag <- "geneCDF"
method <- "fs1_man_fsetid"
}
else if (chip == "Clariom_S_Mouse") {
methodTag <- "TCid"
method <- c("transcriptClusterID", "probeset_list", "geneName", "locus_type", "probesetType", "chr_num", "chr_start", "chr_stop", "chr_strand")
# method <- "transcriptClusterID"
}
else if (chip == "MoGene-1_0-st-v1") {
methodTag <- "TCid"
method <- "transcriptClusterID"
}
info <- probeFile[,.(nProbes = .N), keyby = method]
# Use 'nProbes' to check against 'total_probes' from 'MTA_annot_TCid' from affy
}
else if (method == 2 & chip == "MTA-1_0") {
methodTag <- "exonCDF"
method <- "fs1_man_fsetid"
info <- probeFile[,.(nProbes = .N), keyby = method]
}
else if (method == 3 & chip == "MTA-1_0") {
methodTag <- "D_to_S"
probeFile <- probeFile[!geneName %chin% ""]
method <- "transcriptClusterID"
mergeKey = c(method, "probeID")
info <- probeFile[,.N, keyby = mergeKey][,.(nProbes = .N), keyby = method]
} else stop("NO METHOD APPLIED")
if (!identical(key(info), method)) setkeyv(info, method)
} else if (chip %in% chip430) {
trim <- 0.02
# bgp <- probeFile[probeType %chin% "misMatch"]
bgp <- probeFile[probe_type %chin% "mm"]
# probeFile <- probeFile[probeType %chin% "perfectMatch"]
probeFile <- probeFile[probe_type %chin% "pm"]
if (method == 1) method <- methodTag <- "pmmm"
else if (method == 2) method <- methodTag <- "gc"
# info <- probeFile[,.N, keyby = .(probesetID, probesetName)]
info <- probeFile[,.N, keyby = .(probesetID)]
} else stop("CHIP TYPE NOT FOUND")
if (!identical(key(probeFile), key(info))) {
setkeyv(probeFile, key(info))
setkeyv(bgp, key(info))
# setkey(bgp, probeset_id)
}
cIdx <- length(colnames(info))
infoKey <- key(info)
if (is.character(method)) {
if (!is.null(celTable)) {
for (i in 1:nrow(celTable)) {
print("READING CEL FILES")
cel1 <- readCel(celTable[[2]][i], readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
cel2 <- readCel(celTable[[3]][i], readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
Score <- computeSscore(cel1, cel2, probeFile, bgp, method, SF1 = SF1, SF2 = SF2, verbose = verbose, trim = trim)
info <- info[Score, on = infoKey]
if (celTab.names){
print("Custom run name for BATCH job:")
colnames(info)[cIdx + i] <- as.character(celTable[i,1])
print(as.character(celTable[i,1]))
}
else{
print("Standard run name for BATCH job:")
#colnames(info)[cIdx + i] <- paste("RUN_", i, sep = "")
# Add filenames to colname (CEL_1 vs CEL_2)
celName1 <- strsplit(cel1$header$filename, "/")[[1]]; celName1 <- celName1[length(celName1)]
celName2 <- strsplit(cel2$header$filename, "/")[[1]]; celName2 <- celName2[length(celName2)]
colnames(info)[cIdx + i] <- paste(celName1, "vs", celName2)
print(paste(celName1, "vs", celName2))
}
}
} else if (!is.null(celFile1) & !is.null(celFile2)) {
print("READING CEL FILES")
cel1 <- readCel(celFile1, readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
cel2 <- readCel(celFile2, readIntensities = TRUE, readStdvs = TRUE, readPixels = TRUE, readXY = TRUE)
Score <- computeSscore(cel1, cel2, probeFile, bgp, method, SF1 = SF1, SF2 = SF2, verbose = verbose, trim = trim)
info <- info[Score, on = infoKey]
colnames(info)[cIdx + 1] <- "Sscore"
# Add filenames to colname (CEL_1 vs CEL_2):
# celName1 <- strsplit(cel1$header$filename, "/")[[1]]; celName1 <- celName1[length(celName1)]
# celName2 <- strsplit(cel2$header$filename, "/")[[1]]; celName2 <- celName2[length(celName2)]
# colnames(info)[cIdx + 1] <- paste(celName1, "vs", celName2)
# print("Sscore2 run output assigned to column name:")
# print(paste(celName1, "vs", celName2))
}
# if (verbose) View (info)
}
# Add annotations to ClariomD/MTA arrays:
if (methodTag == "geneCDF" & chip == "MTA-1_0"){
print("Adding gene-level annotations to MTA/ClariomD Sscores")
annot <- fread(gunzip(system.file("extdata","Mouse_ClariomD_TCid_geneCDF_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
setkey(annot,transcript_cluster_id)
info <- annot[info]
info <- info[transcript_cluster_id %like% ".mm.1"]
info <- info[,probeset_id := NULL]
}
if (methodTag == "exonCDF" & chip == "MTA-1_0"){
print("Adding exon-level annotations to MTA/ClariomD Ssscores")
annot <- fread(gunzip(system.file("extdata","Mouse_ClariomD_PSR_exonCDF_affyannot.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
setkey(annot,probeset_id)
info <- annot[info]
info <- info[probeset_id %like% ".mm.1"]
# info <- annot[transcript_cluster_id %like% ".mm.1"]
}
if (methodTag == "D_to_S" & chip == "MTA-1_0"){
print("Adding gene-level annotations for to ClariomD-masked-to-ClariomS Sscores")
annot <- fread(gunzip(system.file("extdata","Mouse_ClariomS_affyyannot_na36.csv.gz",
package = "Sscore2"),remove=FALSE,temporary=TRUE,overwrite=TRUE))
setkey(annot,transcript_cluster_id)
info <- annot[info]
}
if (fileout) {
#ID tag: a custom formatted timestamp applied to all written files
ID <- format(Sys.time(), "%Y%m%d_%H%M%S")
fileName <- paste(chip, "_", methodTag, "_", "Sscore2_", ID, ".csv", sep = "")
print("WRITING S-SCORE OUTPUT TO DIRECTORY")
fwrite(info, fileName)
}
if (gzip) {
print("COMPRESSING SSCORE OUTPUT FILE")
system(paste("gzip", fileName))
}
print("DONE")
# options(warn = 0)
return(info)
}
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