seqcush: Add cushion for sequencing data.

In MonkeyLB/TDR: Estimate the reproducibility of sequencing-based experiment

Description

Add a cushion for sequencing data which reduces the discrepancy of read counts that has no biological meaning but greatly increases the discordance in ranks of the data.

Usage

seqcush(dat, cush)

Arguments

dat	a matrix that has two columns, each of them represent a replicate of data, i.g., sequencing counts for genomic loci.
cush	an integer, the differece in sequencing counts that are deemed the same. For example, if a cush of 2 is chosen, the read count of 4 at a loci of replicate 1 and the read count of 6 at the same loci of replicate 2 are deemed the same. The 6 in replicate 2 is corrected to 4.

Value

This function returns a matrix of two colunms of data, i.g., seqencing counts. Each column is a vector a counts after correction to eliminate the discordance between two replicates in ranks.

Examples

data(Chipseq_TF)
cush <- 2
seqcush(Chipseq_TF, cush)

MonkeyLB/TDR documentation built on May 7, 2019, 4:59 p.m.