NCIS: NCIS

In yancychy/DiffChIPL: ChIP-seq differential analysis (DiffChIPL)

NCIS

Description

Estimates normalizing factor between a ChIP sample and a control/input sample

Usage

NCIS(chip.data, input.data, data.type = c("MCS", "BED", "AlignedRead", "BAM"), frag.len = 200, min.binsize = 100, max.binsize = 20000, binsize.shift = 100, min.stop.binsize = 100, chr.vec = NULL, chr.len.vec = NULL, quant=0.75)

Arguments

chip.data	ChIP data. For BAM file format, it is an string to represent bam file path
input.data	control data. For BAM file format, it is an string to represent bam file path
data.type	"MCS", "AlignedRead", "BED" or "BAM".
frag.len	average fragment length. Default 200 bp.
min.binsize	minimum of binsize to search.
max.binsize	maximum of binsize to search.
binsize.shift	the threshold of binsize after which the normalization factor is computed as the average of two estimates, one on regular bins and the other on bins shifed half binsize.
min.stop.binsize	minimum of binsize to use (stop).
chr.vec	vector of chromosomes in the data. Only reads in chr.vec are considered for normalization purpose.
chr.len.vec	vector of chromosome lengths corresponding to chr.vec
quant	quantile to start the searching for total threshold. Default 0.75.

Details

data.type

• MCS Minimum ChIP-Seq format. data.frame with fields: chr (factor), pos (integer) and strand (factor, "+" and "-"). pos is 5' location. This is different from eland default which use 3' location for reverse strand.

• AlignedRead from Bioconductor ShortRead package (with support of commonly used formats, including Eland, MAQ, Bowtie, SOAP and BAM).

• BED with at least first 6 fields (chrom, start, end, name, score and strand), http://genome.ucsc.edu/FAQ/FAQformat.html#format1.

Value

A list with following components:

est	the estimated normalizing factor.
binsize.est	the estimated binsize.
r.seq.depth	sequencing depth ratio.
pi0	the estimated proportion of background reads among ChIP sample.

Author(s)

Kun Liang, [e-mail]

References

Liang, K and Keles, S (2012). Normalization of ChIP-seq data with control, to appear.

Examples

data("SEG3")
res <- NCIS(chip.data, input.data, data.type="MCS")
res

yancychy/DiffChIPL documentation built on Dec. 24, 2024, 11:26 p.m.