Description Usage Arguments Details Value Author(s) References
View source: R/mixNBHMMDataSetFromBam.R
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.
1 2 3 4 5 6 7 8 | mixNBHMMDataSetFromBam(
bamFiles,
colData,
genome,
blackList,
windowSize,
fragLength = NULL
)
|
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 |
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. |
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.
A (RangedSummarizedExperiment) mixNBHMMDataSet
Pedro L. Baldoni, pedrobaldoni@gmail.com
Nucleic Acids Research 44, e45 (2015).
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