prepareTximportFiles: Prepare quant files for tximport

In steinbaugh/DESeqAnalysis: DESeq2 Analysis Utilities

Description

Prepare quant files for tximport

Usage

prepareTximportFiles(
  files,
  makeNames = c("makeNames", "snakeCase", "camelCase"),
  exists = TRUE
)

Arguments

files	character. Quant file paths (e.g. "quant.sf" for salmon, "abundance.h5" for kallisto). See tximport() for details.
makeNames	character(1). Syntactic name function to apply on sample names. Uses match.arg() internally. See basejump toolkit for details.
exists	logical(1). Check if requested input exists on disk. Runs realpath() 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 2019-10-09.

Examples

files <- c(
    file.path("salmon", "1-sample-A", "quant.sf"),
    file.path("salmon", "2-sample-B", "quant.sf")
)
print(files)
files <- prepareTximportFiles(files, makeNames = "snakeCase", exists = FALSE)
print(files)

steinbaugh/DESeqAnalysis documentation built on Sept. 25, 2020, 5:21 a.m.