prepareTximportFiles: Prepare quant files for tximport

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Prepare quant files for tximport

Description

Prepare quant files for tximport

Usage

prepareTximportFiles(
  dir,
  type = c("salmon", "kallisto"),
  makeNames = c("makeNames", "snakeCase", "camelCase")
)

Arguments

dir	character(1). Directory path containing quant files. See tximport() for details.
type	character(1). Type of quant/abundance file to find. Expecting "quant.sf" for salmon, "abundance.h5" for kallisto.
makeNames	character(1). Syntactic name function to apply on sample names. Uses match.arg() internally.

Details

Runs the following internal comments:

1. Extract sample directory name from quant file using dirname() and basename().

2. Autopad zeros, if necessary, via autopadZeros().

3. Sanitizes names with snakeCase().

4. Sorts files alphabetically.

Value

character. Return quant file paths, with valid sample names automatically applied.

Note

Updated 2023-07-13.

See Also

• tximport vignette

Examples

suppressPackageStartupMessages({
    library(AcidBase)
})
tempdir <- tempdir2()
samples <- c("1-sample-A", "2-sample-B")
salmonDir <- initDir(file.path(tempdir, "salmon"))
kallistoDir <- initDir(file.path(tempdir, "kallisto"))
invisible({
    lapply(X = file.path(salmonDir, samples), FUN = initDir)
    file.create(file.path(salmonDir, samples, "quant.sf"))
    lapply(X = file.path(kallistoDir, samples), FUN = initDir)
    file.create(file.path(kallistoDir, samples, "abundance.h5"))
})
salmonFiles <- prepareTximportFiles(dir = salmonDir, type = "salmon")
print(salmonFiles)
kallistoFiles <- prepareTximportFiles(dir = kallistoDir, type = "kallisto")
print(kallistoFiles)
unlink2(tempdir)

acidgenomics/DESeqAnalysis documentation built on March 27, 2024, 10:32 p.m.