DNaseHiC: Methods for processing DNase Hi-C data

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Processing of BAM files for DNase Hi-C into index files

Usage

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emptyGenome(bs)

# Deprecated
segmentGenome(bs) 

# Deprecated
prepPseudoPairs(bam, param, file, dedup=TRUE, minq=NA, ichim=TRUE, 
    chim.span=1000, output.dir=NULL, storage=5000L)

Arguments

bs

a BSgenome object, or a character string pointing to a FASTA file, or a named integer vector of chromosome lengths

bam

a character string containing the path to a name-sorted BAM file

param

a pairParam object containing read extraction parameters

file

a character string specifying the path to an output index file

dedup

a logical scalar indicating whether marked duplicate reads should be removed

minq

an integer scalar specifying the minimum mapping quality for each read

ichim

a logical scalar indicating whether invalid chimeras should be counted

chim.span

an integer scalar specifying the maximum span between a chimeric 3' end and a mate read

output.dir

a character string specifying a directory for temporary files

storage

an integer scalar specifying the maximum number of pairs to store in memory before writing to file

Details

DNase Hi-C uses DNase to randomly fragment the genome, rather than using restriction fragments. This requires some care to handle in diffHic, as most functions rely on fragment assignments in many functions. To specify that the data are from a DNase Hi-C experiment, an empty GRanges object should be supplied as the fragments in pairParam. Most functions will automatically recognise that the data are DNase Hi-C and behave appropriately. This reflects the fact that no restriction fragments are involved in this analysis. Genome information will instead be extracted from the seqlengths of the GRanges object.

prepPseudoPairs and segmentGenome are deprecated in favour of preparePairs and emptyGenome, respectively. In the case of preparePairs, it will automatically detect if the BAM file is to be treated as DNase Hi-C based on param$fragments.

Value

For emptyGenome, an empty GRanges object is produced containing the sequence names and lengths.

Author(s)

Aaron Lun

See Also

preparePairs, cutGenome

Examples

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require(BSgenome.Ecoli.NCBI.20080805)
emptyGenome(Ecoli)
emptyGenome(c(chrA=100, chrB=200))

diffHic documentation built on April 29, 2020, 2:08 a.m.