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Last data update: 2014.03.03
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R: Convert BAM files into BED files containing the reads...
| bam_to_reads | R Documentation |
Convert BAM files into BED files containing the reads overlaping the specified annotations.
Description
Convert BAM files into BED files containing the reads overlaping the specified annotations.
Usage
bam_to_reads(bamfile, annotations, paired_end = TRUE, as_fragments = TRUE,
outfile = NULL, flanking_region = 0)
Arguments
bamfile |
a character vector indicating the BAM file name.
Note: The bamfile must be sorted by coordinates.
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annotations |
an object of type annotationsSet
containing information on one genes.
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paired_end |
logical indicating whether the bamfile
contains paired-end data.
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as_fragments |
logical indicating if paired-end data must be paired
and merged to form fragments.
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outfile |
a character vector indicating the output file name.
If not provided, the result will be internalized in R.
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flanking_region |
Number of bases before and after the gene ORF should be included.
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Value
An object of type data.table with 9 columns.
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chromosome | Read chromosome. |
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start | Read starting position. |
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end | Read ending position. |
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name | Query template name . |
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score | Mapping quality. |
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ChromosomeNext | Gene strand. |
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startNext | Position of the mate/next read. |
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tlen | observed read length. |
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flag | bitwise flag.
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Examples
bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
data(annotations)
bam_to_reads(bamfile, annotations)
Results
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providing 
.