peak_target_matrix: Peak target gene matrix for multiple samples

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

This function generates gene based peak target matrix for multiple samples. If sampleInfo has just one row for a sample, this function will return per gene peak target for just one sample. If there are multiple samples, a full join is performed to extract peaks in all samples for each gene.

Usage

peak_target_matrix(sampleInfo, position = "TSS")

Arguments

sampleInfo	sample information dataframe
position	One of c("TSS", "TES", "best", "both"). This is used for filtering the target genes for each sample. Default: "TSS". Refer to Details section for more information.

Details

A gene can have two types of peaks, one at TSS and another at TES. position option allows to select the peak target in following manner.

• TSS: select genes with peak signal upstream or near TSS

• TES: select genes with peak signal near end of the gene

• best: If a gene have both TSS and TES region peak, select best based on log10Pvalue of peak caller

• both: If a gene have both TSS and TES region peak, select both peaks

Value

A gene wise peak target dataframe for multiple samples

Examples

NA

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.