getMATfromDataFrame: Helper function to turn a data.frame into a matrix and remove...

In DChIPRep: DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

Description

This function takes a data.frame, with the genomic features (e.g. transcripts or genes) in the rows and the positions upstream and downstream of the TSS in the columns as well as a column ID containing a genomic feature ID and returns the data.frame with the ID column removed. The input for this function are tables obtained after running the Python import script.

Usage

getMATfromDataFrame(df, ID = "name")

Arguments

df	the input data frame with positions in the columns and the genomic features in the rows.
ID	the name of the ID column to be removed.

Value

a matrix with the ID column removed

Examples

data(exampleSampleTable)
directory <- file.path(system.file("extdata", package="DChIPRep"))
df  <- lapply(file.path(directory, exampleSampleTable$Input), 
read.delim)[[1]]
mat <- getMATfromDataFrame(df)

DChIPRep documentation built on April 29, 2020, 4:26 a.m.