Genome Organisation Through HiC from HiCUP output

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Description

GOTHiChicup performs a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped and filtered paired NGS reads from HiCUP as input and gives back the list of significant interactions for a given bin size in the genome.

Usage

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GOTHiChicup(fileName, sampleName, res, restrictionFile, cistrans='all', parallel=FALSE, cores=NULL)

Arguments

fileName

A character string with the name of the file containing the mapped, filtered reads from HiCUP, after the default HiCUP output is converted to a table containing only the read ID, chromosome, start and end positions columns. Can be gzipped. (Tab separated text format)

sampleName

A character string that will be used to name the quality control plot. It will be saved in the current directory.

res

An integer that gives the required bin size or resolution of the contact map e.g. 1000000, for fragment level use 1.

restrictionFile

A character string with the name of the digest file from HiCUP. It is used to map reads to restriction fragments. (.txt file name)

cistrans

A character string with three possibilities. "all" runs the binomial test on all interactions, "cis" runs the binomial test only on intrachromosomal/cis interactions, "trans" runs the binomial test only on interchromosomal/trans interactions.

parallel

Logical argument. If TRUE the mapping and the binomial test will be performed faster using multiple cores. The default is FALSE.

cores

An integer specifying the number of cores used in the parallel processing if parellel=TRUE. The default is NULL.

Value

A data.frame containing elements

chr1 / chr2

chromosome(s) containing interacting regions 1 and 2

locus1 / locus2

start positions of the interacting regions 1 and 2 in the corresponding chromosome(s)

relCoverage1 / relCoverage2

relative coverage corresponding to regions 1 and 2

probability

expected frequency

expected

expected number of reads

readCount

observed reads number

pvalue

binomial p-value

qvalue

binomial p-value corrected for multi-testing with Benjamini-Hochberg

logObservedOverExpected

observed/expected read numbers log ratio

Author(s)

Borbala Mifsud and Robert Sugar

See Also

binom.test

Examples

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library(GOTHiC)
dirPath <- system.file("extdata", package="HiCDataLymphoblast")
fileName <- list.files(dirPath, full.names=TRUE)[4]
restrictionFile <- list.files(dirPath, full.names=TRUE)[3]
binom=GOTHiChicup(fileName, sampleName='lymphoid_chr20', res=1000000, 
restrictionFile, cistrans='all', parallel=FALSE, cores=NULL)