shiftPromoter: Select genes which have core promoter shift across different...

In Linlab-slu/TSSr: TSS sequencing data analysis

Select genes which have core promoter shift across different experiments.

Description

Selects genes which have multiple core promoters and undergo core promoter shifting across different experiments. Generates gene list with Ds (degree of shift) value (Lu et al., 2019), p value and adjusted p value.

Usage

shiftPromoter(object, comparePairs, pval=0.01)

## S4 method for signature 'TSSr'
shiftPromoter(object, comparePairs, pval = 0.01)

Arguments

object	A TSSr object.
comparePairs	Specified list of sample pairs for comparison.
pval	Genes with adjusted p value >= pval will be returned. Default value = 0.01.

Value

Large List of elements - one element for each sample

Examples

data(exampleTSSr)
#shiftPromoter(exampleTSSr,comparePairs=list(c("control","treat")), pval = 0.01)

Linlab-slu/TSSr documentation built on Oct. 24, 2023, 8:32 p.m.