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#!/usr/bin/env RScript
#contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
#email="m_gruenstaeudl@fhsu.edu"
#version="2024.04.08.0223"
writeCovTables <- function(covData, sample_name, dir) {
writeStatsTable(covData$ir_genes, sample_name, dir, "coverage.genes")
writeStatsTable(covData$ir_regions, sample_name, dir, "coverage.regions")
writeStatsTable(covData$ir_noncoding, sample_name, dir, "coverage.noncoding")
}
writeStatsTable <- function(df, sample_name, dir, fileName) {
write.table(
df,
paste(dir, .Platform$file.sep, sample_name["sample_name"], "_", fileName, ".tsv", sep = ""),
row.names = FALSE,
quote = FALSE,
sep = "\t"
)
}
writeSumTables <- function(summary, sample_name, dir) {
sumField2File <- getSumField2File()
for (sumField in names(summary)) {
sumFile <- sumField2File[[sumField]]
writeStatsTable(summary[[sumField]], sample_name, dir, sumFile)
}
}
getSumField2File <- function() {
sumField2File <- list(
"regions_summary" = "summary.regions",
"genes_summary" = "coverage.summary.genes",
"noncoding_summary" = "coverage.summary.noncoding"
)
return(sumField2File)
}
printCovStats <- function(gbkData,
coverageRaw,
analysisSpecs,
outputSpecs) {
sampleName <- gbkData$sampleName
seqnames <- unname(sampleName[sampleName %in% names(coverageRaw)])
if (length(seqnames) == 0) {
logger::log_error("Neither `ACCESSION` nor `VERSION` matches BAM sample name")
return(NULL)
}
logger::log_info('Generating statistical information on the sequencing coverage')
quadripRegions <- gbkData$quadripRegions
genes <- gbkData$genes
covData <- getCovData(quadripRegions, genes)
covData <- filter_IR_genes(quadripRegions, coverageRaw, seqnames, covData, analysisSpecs)
covData <- filter_IR_noncoding(quadripRegions, coverageRaw, seqnames, covData, analysisSpecs)
covData <- filter_IR_regions(coverageRaw, seqnames, covData, analysisSpecs)
covData <- setLowCoverages(covData, analysisSpecs)
# Writing values to output table
statsFilePath <- outputSpecs$statsFilePath
writeCovTables(covData,
sampleName,
statsFilePath)
return(covData)
}
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