A data.frame or an AnnotatedDataFrame object
containing bin annotations.
bamfiles
A character vector of (BAM) file names. If NULL (default),
all files with extension ext, are read from directory path.
path
If bamfiles is NULL, directory path to read input files from.
Defaults to the current working directory.
ext
File name extension of input files to read, default is "bam".
bamnames
An optional character vector of sample names. Defaults to
file names with extension ext removed.
phenofile
An optional character(1) specifying a file name for
phenotype data.
chunkSize
An optional integer specifying the chunk size (nt) by
which to process the bam file.
cache
Whether to read and write intermediate cache files, which
speeds up subsequent analyses of the same files. Requires packages
R.cache and digest (both available on CRAN) to be installed. Defaults
to getOption("QDNAseq::cache", FALSE).
force
When using the cache, whether to force reading input data
from the BAM files even when an intermediate cache file is present.
isPaired
A logical(1) indicating whether unpaired (FALSE), paired
(TRUE), or any (NA, default) read should be returned.
isProperPair
A logical(1) indicating whether improperly paired
(FALSE), properly paired (TRUE), or any (NA, default) read should be
returned. A properly paired read is defined by the alignment algorithm
and might, e.g., represent reads aligning to identical reference
sequences and with a specified distance.
isUnmappedQuery
A logical(1) indicating whether unmapped
(TRUE), mapped (FALSE, default), or any (NA) read should be returned.
hasUnmappedMate
A logical(1) indicating whether reads with mapped
(FALSE), unmapped (TRUE), or any (NA, default) mate should be
returned.
isMinusStrand
A logical(1) indicating whether reads aligned to
the plus (FALSE), minus (TRUE), or any (NA, default) strand should be
returned.
isMateMinusStrand
A logical(1) indicating whether mate reads
aligned to the plus (FALSE), minus (TRUE), or any (NA, default) strand
should be returned.
isFirstMateRead
A logical(1) indicating whether the first mate
read should be returned (TRUE) or not (FALSE), or whether mate read
number should be ignored (NA, default).
isSecondMateRead
A logical(1) indicating whether the second mate
read should be returned (TRUE) or not (FALSE), or whether mate read
number
should be ignored (NA, default).
isSecondaryAlignment
A logical(1) indicating whether alignments
that are primary (FALSE), are not primary (TRUE) or whose primary
status does not matter (NA, default) should be returned. A non-primary
alignment ("secondary alignment" in the SAM specification) might
result when a read aligns to multiple locations. One alignment is
designated as primary and has this flag set to FALSE; the remainder,
for which this flag is TRUE, are designated by the aligner as
secondary.
isNotPassingQualityControls
A logical(1) indicating whether
reads passing quality controls (FALSE, default), reads not passing
quality controls (TRUE), or any (NA) read should be returned.
isDuplicate
A logical(1) indicating that un-duplicated
(FALSE, default), duplicated (TRUE), or any (NA) reads should be
returned. 'Duplicated' reads may represent PCR or optical duplicates.
minMapq
If quality scores exists, the minimum quality score
required in order to keep a read, otherwise all reads are kept.
pairedEnds
A boolean value or vector specifying whether the BAM
files contain paired-end data or not. Only affects the calculation of
the expected variance.
Value
Returns a QDNAseqReadCounts object with assay data element
counts containing the binned read counts as non-negative integers.
Author(s)
Ilari Scheinin, Daoud Sie
Examples
## Not run: # read all files from the current directory with names ending in .bam
bins <- getBinAnnotations(15)
readCounts <- binReadCounts(bins)
## End(Not run)