readS: read S

Description Usage Arguments Details Value Author(s)

View source: R/functions.R

Description

This function reads and annotates matrix S.

Usage

1
  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


Bioconductor-mirror/MineICA documentation built on May 29, 2017, 8:30 a.m.