count.everted.reads: Count the number of everted reads for a set of BAM files.
This is the ExomeDepth high level function that takes a GenomicRanges
object, a list of indexed/sorted BAM files, and compute the number of
everted reads in each of the defined bins.
data.frame containing the definition of the
The first three columns must be chromosome, start, end.
character file name. Target BED file with the
definition of the regions. This file will only be used if no bed.frame
argument is provided. No headers are assumed so remove them if they
exist. Either a bed.file or a bed.frame must be provided for this
function to run.
character, list of BAM files to extract read count data from.
character argument with the list of indexes for the BAM files, without the
'.bai' suffix. If the indexes are simply obtained by adding .bai to
the BAM files, this argument does not need to be specified.
numeric, minimum mapping quality to include a read.
logical, if set to TRUE, this function will remove the string 'chr' from the
chromosome names of the target BED file.
Everted reads are characteristic of the presence of duplications in a
BAM files. This routine will parse a BAM files and the suggested use
is to provide relatively large bins (for example gene based, and
ExomeDepth has a genes.hg19 object that is appropriate for this) to
flag the genes that contain such reads suggestive of a duplication. A
manual check of the data using IGV is recommended to confirm that
these reads are all located in the same DNA region, which would
confirm the presence of a copy number variant.
A data frame that contains the region and the number of identified
reads in each bin.
This function calls a lower level function called XXX that works on each
single BAM file.
Computational methods for discovering structural variation with
next-generation sequencing, Medvedev P, Stanciu M, Brudno M., Nature
## Not run: test <- count.everted.reads (bed.frame = genes.hg19,
bed.file = NULL,
bam.files = bam.files,
min.mapq = 20,
include.chr = FALSE)
## End(Not run)