E3MakeFCSegmentation: Perform genomic segmentation.

In tkonopka/ExpCube: Analysis of cell/stimulus/gene expression data

Description

This function uses CBS (package DNAcopy) to segment genomic data. This wrapper allows to start with a data matrix containing values associated with gene names. A separated object mapping genes to genomic positions is used to arrange the data before segmentation.

Usage

E3MakeFCSegmentation(fcdata, gene.position = NULL, genenames = NULL,
  chrnames = NULL, min.width = 5, verbose = TRUE)

Arguments

fcdata	- numeric matrix with sample names in colnames and gene names in rownames.
gene.position	- data frame with columns "chr", "pos", and rownames containing gene names.
genenames	- names of
chrnames	- character vector with names of chromosomes to include in segmentation. Leave null, To use all the genes in the input matrix.
min.width	- minimum number
verbose	- logical. When TRUE, function prints dots indicating progress.

Details

Values in fcdata will be log2 transformed before being sent to segmentation. Functions returns a list with the resulting segmentation.

tkonopka/ExpCube documentation built on May 31, 2019, 3:44 p.m.