mixNBHMMDataSetFromBam: Create a mixNBHMMDataSet from a set of BAM files

In plbaldoni/mixNBHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

Description

This function creates a (RangedSummarizedExperiment) mixNBHMMDataSet object out of a set of BAM files. It assumes that the BAM files have been through all the necessary pre-processing steps for ChIP-seq data analysis, such as low quality read filtering and PCR duplicate removal.

Usage

mixNBHMMDataSetFromBam(
  bamFiles,
  colData,
  genome,
  blackList,
  windowSize,
  fragLength = NULL
)

Arguments

bamFiles	a set of paths from sorted and indexed BAM files. The index files must be located in the same directory of their respective bam files. The index files must be named like their respective bam file with the additional “.bai” suffix
colData	a data frame with the information about the bamFiles. It should contain two named columns Condition and Replicate referring to the experimental conditions and their replicate identifiers.
genome	either 'hg19' or a GRanges object with the chromosome lengths of the reference genome (see details)
blackList	either 'hg19', NULL, or a GRanges object with the genomic coordinates to be removed (see details). If NULL, no genomic regions will be discarded.
windowSize	an integer specifying the size of genomic windows where read counts will be computed
fragLength	either a vector of estimated fragment lengths relative to the bamFiles experiments, or NULL (default). If NULL, it will be estimated using csaw cross-correlation analysis with default parameters.

Details

If genome='hg19', this function will compute read counts using the reference genome hg19 from the package BSgenome.Hsapiens.UCSC.hg19 on chromosomes 1,...,22,X,Y in common across all experiments. Otherwise, genome should be a GRanges object with chromosome names (seqnames), start positions (start), and end positions (end).

If blackList='hg19', this function will exclude genomic coordinates pertaining to blacklisted regions defined in https://github.com/Boyle-Lab/Blacklist/tree/master/lists. See https://sites.google.com/site/anshulkundaje/projects/blacklists for a detailed discussion and recommendations.

Value

A (RangedSummarizedExperiment) mixNBHMMDataSet

Author(s)

Pedro L. Baldoni, [e-mail]

References

Nucleic Acids Research 44, e45 (2015).

plbaldoni/mixNBHMM documentation built on Dec. 24, 2019, 1:31 p.m.