readS: read S

In bitona/MineICA: Analysis of an ICA decomposition obtained on genomics data

read S

Description

This function reads and annotates matrix S.

Usage

  readS(Sfile, datfile, dat, annot = TRUE)

Arguments

Sfile	The file which contains the matrix of feature projections. It must be a txt file where the separator is white space, that is one or more spaces, tabs, newlines or carriage returns.
datfile	The file which contains the matrix (of dimension features x samples) based on which the matrix S was calculated. It must be a txt file where the separator is white space, that is one or more spaces, tabs, newlines or carriage returns.
dat	The data based on which the matrix A was calculated (features x samples)
annot	TRUE (default) if the Afile contains rownames of matrix A, FALSE if the rownames has to be extracted from dat

Details

The matrix dat must be the one on which the matrix S was calculated. It is assumed that the number of components is lower than the number of features, the matrix will be transposed to have dimension 'features x components' according to this assumption. If annot is FALSE, rownames of dat are used to annotate rownames of S.

Value

This function returns a matrix of dimension features x components with rownames filled with feature IDs.

Author(s)

Anne Biton

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.