loadCountData: Load count files

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

Load count files

Description

Load one count file per sample thanks to the file names in the target file.

Usage

loadCountData(
  target,
  rawDir = "raw",
  skip = 0,
  featuresToRemove = c("alignment_not_unique", "ambiguous", "no_feature",
    "not_aligned", "too_low_aQual")
)

Arguments

target	target data.frame of the project returned by loadTargetFile()
rawDir	path to the directory containing the count files
skip	number of lines of the data file to skip before beginning to read data
featuresToRemove	vector of feature Ids (or character string common to feature Ids) to remove from the counts

Details

If featuresToRemove is equal to "rRNA", all the features containing the character string "rRNA" will be removed from the counts.

Value

The matrix of raw counts with row names corresponding to the feature Ids and column names to the sample names as provided in the first column of the target.

Author(s)

Marie-Agnes Dillies and Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.