reorder.samples.computeMatrix: Sample reorderer computeMatrix file

In sebastian-gregoricchio/Rseb: An R-package for NGS data managing and visualization

Sample reorderer computeMatrix file

Description

A tool to reorder the samples in a computeMatrix file avoiding the re-computation of the latter.

Usage

## S3 method for class 'samples.computeMatrix'
reorder(
  matrix.file,
  new.sample.order = NULL,
  reordered.matrix.path = gsub(".gz", "_reordered.gz", matrix.file),
  ignore.header.error = FALSE,
  verbose = TRUE
)

Arguments

matrix.file	String with the full path to a deeptools computeMatrix .gz file.
new.sample.order	String vector with the sample labels in the order in which they should appear in the matrix. By default NULL, which returns a message with the sample labels in the original order. Further, it returns the vector with the original sample order.
reordered.matrix.path	String with full path to for the file of the reorder matrix (.gz). By default the output name will be <original.matrix.name>_reordered.gz.
ignore.header.error	Logical value to indicate whether the error of sample_label reassignment in the header should be ignored. The plotted labels can be changed during the plotting.
verbose	Logical value to indicate whether the final message should be printed. By default TRUE.

Value

The output is a computeMatrix file (.gz format) with the samples chucks re-shuffled to be in the order provided by the user.

sebastian-gregoricchio/Rseb documentation built on Sept. 4, 2024, 1:59 p.m.