copar.Aligner: ChIP-seq Optimal Peak Alinger

In gladex/COPAR: ChIP-seq Optimal Peak AnalyzeR

Description

copar.Aligner is the package function to detect the optimal peak candiate from the raw ChIP-seq input data (in BED format).

Usage

Main steps to run copar.Aligner:

The function can only run in Linux environment:

(1) The engine package "BELT1.0.2_linux64" and input data should be located on the reachable directories, e.g. ./BELT1.0.2_linux64, ./InputData.bed.

(2) Open R (in Linux), and run:
copar.Aligner(hg = "hg18",
             ws = seq(from = 100, to = 500, by = 50),
             pv = seq(from = 0.951, to = 0.999, by = 0.003),
             bf = "SRR015350_Sorted.bed",
             otf = "SRR015350_copa")

Arguments

hg	Reference genome, e.g. mm9, hg18, hg19, etc.
ws	Windows size, e.g. 100,150,200, etc.
pv	P-value threshold, e.g. 0.951, 0.954, etc.
bf	Input file of BED format, e.g., bf = "SRR015350_Sorted.bed".
otf	Output file name, e.g. otf = "SRR015350_copa".

Author(s)

Binhua Tang <[e-mail]>

References

1. Tang B, Hsu H-K, Hsu P-Y, Bonneville R, Chen S-S, Huang TH-M, et al. Hierarchical modularity in ER¦Á transcriptional network is associated with distinct functions and implicates clinical outcomes. NPG Scientific Reports. 2012;2.

Examples

library(COPAR)
## check the help docs.
?copar.Aligner
## run the copar.Aligner
copar.Aligner(hg = "hg18",
             ws = seq(from = 100, to = 500, by = 50),
             pv = seq(from = 0.951, to = 0.999, by = 0.003),
             bf = "SRR015350_Sorted.bed",
             otf = "SRR015350_copa")

gladex/COPAR documentation built on Sept. 12, 2021, 1:07 p.m.