DNaseHiC {diffHic} | R Documentation

## 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))

[Package diffHic version 1.20.0 Index]