qExportWig(proj, file=NULL, collapseBySample=TRUE, binsize=100L, shift=0L, strand=c("*","+","-"), scaling=TRUE, tracknames=NULL, log2p1=FALSE, colors=c("#1B9E77", "#D95F02", "#7570B3", "#E7298A", "#66A61E", "#E6AB02", "#A6761D", "#666666"), includeSecondary=TRUE, mapqMin=0L, mapqMax=255L, absIsizeMin=NULL, absIsizeMax=NULL, createBigWig=FALSE)qProject object as returned by qAlign.NULL or a vector of the same
length as the number of bam files (for
collapseBySample=FALSE) or the number of unique sample names
(for collapseBySample=TRUE) in proj. If NULL, the
wig or bigWig file names are generated from the names of the genomic
bam files or unique sample names with an added “.wig.gz” or
“.bw” extension.TRUE, genomic bam files with identical
sample name will be combined (summed) into a single track.binsize will be coerced to
integer().length(shift)>1,
the length must match the number of bam files in ‘proj’, and
the i-th sample will be converted to wig or bigWig using the value in
shift[i]. shift will be coerced to integer(). For
paired-end alignments, shift will be ignored, and a warning
will be issued if it is set to a non-zero value (see ‘Details’).strand. The default (“*”)
will count all alignments.NULL, the sample
names in proj will be used.TRUE, the number of alignments x per bin will
be transformed using the formula log2(x+1).TRUE (the default), include alignments
with the secondary bit (0x0100) set in the FLAG.mapqMin). Valid values are between 0 and 255. The default (0)
will include all alignments.mapqMax). Valid values are between 0 and 255. The default
(255) will include all alignments.NULL (default),
which will not apply any minimum insert size filtering.NULL (default),
which will not apply any maximum insert size filtering.TRUE, first a temporary wig file will be
created and then converted to BigWig format (file extension
“.bw”) using the wigToBigWig
function from package rtracklayer.qExportWig() uses the genome bam files in proj as input
to create wig or bigWig files with the number of alignments (pairs)
per window of binsize nucleotides. By default
(collapseBySample=TRUE), one file per unique sample will be
created. If collapseBySample=FALSE, one file per genomic bam
file will be created. See http://genome.ucsc.edu/goldenPath/help/wiggle.html for the
definition of the wig format, and
http://genome.ucsc.edu/goldenPath/help/bigWig.html for the
definition of the bigWig format.
The genome is tiled with sequential windows of length binsize,
and alignments in the bam file are assigned to these windows: Single
read alignments are assigned according to their 5'-end coordinate
shifted by shift towards the 3'-end (assuming that the 5'-end
is the leftmost coordinate for plus-strand alignments, and the rightmost
coordinate for minus-strand alignments). Paired-end alignments are
assigned according to the base in the middle between the leftmost and
rightmost coordinates of the aligned pair of reads. Each pair of reads
is only counted once, and not properly paired alignments are
ignored. Secondary alignments can be excluded by setting
includeSecondary=FALSE. In paired-end experiments,
absIsizeMin and absIsizeMax can be used to select
alignments based on their insert size (TLEN field in SAM Spec v1.4). For scaling=TRUE, the number of alignments per bin $n$
for the sample $i$ are linearly scaled to the mean total
number of alignments over all samples in proj according to:
$n_s = n /N[i] *mean(N)$ where $n_s$ is the scaled number
of alignments in the bin and $N$ is a vector with the total
number of alignments for each sample. Alternatively, if scaling is set
to a positive numerical value $s$, this value is used instead of
$mean(N)$, and values are scaled according
to: $n_s = n /N[i] *s$.
mapqMin and mapqMax allow to select alignments
based on their mapping qualities. mapqMin and mapqMax can
take integer values between 0 and 255 and equal to
$-10
log10 Pr(mapping position is wrong)$, rounded to the nearest
integer. A value 255 indicates that the mapping quality is not available.
If createBigWig=FALSE and file ends with ‘.gz’,
the resulting wig file will be compressed using gzip and is suitable
for uploading as a custom track to your favorite genome browser
(e.g. UCSC or Ensembl).
qProject, qAlign,
wigToBigWig
# copy example data to current working directory
file.copy(system.file(package="QuasR", "extdata"), ".", recursive=TRUE)
# create alignments
sampleFile <- "extdata/samples_chip_single.txt"
genomeFile <- "extdata/hg19sub.fa"
proj <- qAlign(sampleFile, genomeFile)
# export wiggle file
qExportWig(proj, binsize=100L, shift=0L, scaling=TRUE)
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