windowPerReadLength | R Documentation |
This is defined as: Fraction of reads per read length, per position in whole window (defined by upstream and downstream) If tx is not NULL, it gives a metaWindow, centered around startSite of grl from upstream and downstream. If tx is NULL, it will use only downstream , since it has no reference on how to find upstream region. The exception is when upstream is negative, that is, going into downstream region of the object.
windowPerReadLength(
grl,
tx = NULL,
reads,
pShifted = TRUE,
upstream = ifelse(!is.null(tx), ifelse(pShifted, 5, 20), min(ifelse(pShifted, 5, 20),
0)),
downstream = ifelse(pShifted, 20, 5),
acceptedLengths = NULL,
zeroPosition = upstream,
scoring = "transcriptNormalized",
weight = "score",
drop.zero.dt = FALSE,
append.zeroes = FALSE,
windows = startRegion(grl, tx, TRUE, upstream, downstream)
)
grl |
a |
tx |
default NULL, a GRangesList of transcripts or (container region), names of tx must contain all grl names. The names of grl can also be the ORFik orf names. that is "txName_id" |
reads |
a |
pShifted |
a logical (TRUE), are Ribo-seq reads p-shifted to size 1 width reads? If upstream and downstream is set, this argument is irrelevant. So set to FALSE if this is not p-shifted Ribo-seq. |
upstream |
an integer (5), relative region to get upstream from. Default:
|
downstream |
an integer (20), relative region to get downstream from. Default:
|
acceptedLengths |
an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted. |
zeroPosition |
an integer DEFAULT (upstream), what is the center point? Like leaders and cds combination, then 0 is the TIS and -1 is last base in leader. NOTE!: if windows have different widths, this will be ignored. |
scoring |
a character (transcriptNormalized), which meta coverage scoring ? one of (zscore, transcriptNormalized, mean, median, sum, sumLength, fracPos), see ?coverageScorings for more info. Use to decide a scoring of hits per position for metacoverage etc. Set to NULL if you do not want meta coverage, but instead want per gene per position raw counts. |
weight |
(default: 'score'), if defined a character name of valid meta column in subject. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. ORFik ofst, bedoc and .bedo files contains a score column like this. As do CAGEr CAGE files and many other package formats. You can also assign a score column manually. |
drop.zero.dt |
logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently) |
append.zeroes |
logical, default FALSE. If TRUE and drop.zero.dt is TRUE and all windows have equal length, it will add back 0 values after transformation. Sometimes needed for correct plots, if TRUE, will call abort if not all windows are equal length! |
windows |
the GRangesList windows to actually check, default:
|
Careful when you create windows where not all transcripts are long enough, this function usually is used first with filterTranscripts to make sure they are of all of valid length!
a data.table with 4 columns: position (in window), score, fraction (read length). If score is NULL, will also return genes (index of grl). A note is that if no coverage is found, it returns an empty data.table.
Other coverage:
coverageScorings()
,
metaWindow()
,
regionPerReadLength()
,
scaledWindowPositions()
cds <- GRangesList(tx1 = GRanges("1", 100:129, "+"))
tx <- GRangesList(tx1 = GRanges("1", 80:129, "+"))
reads <- GRanges("1", seq(79,129, 3), "+")
windowPerReadLength(cds, tx, reads, scoring = "sum")
windowPerReadLength(cds, tx, reads, scoring = "transcriptNormalized")
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