DNaseHiC: Methods for processing DNase Hi-C data

In LTLA/diffHic: Differential Analysis of Hi-C Data

Methods for processing DNase Hi-C data

Description

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

Usage

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

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

LTLA/diffHic documentation built on Dec. 20, 2024, 7:06 p.m.