windowPerReadLength {ORFik} | R Documentation |
This is like a more detailed floss score, where floss score takes fraction of reads per read length over whole window, this is defined as: Fraction of reads per read length, per position in whole window (by upstream and downstream)
windowPerReadLength(grl, tx = NULL, reads, pShifted = TRUE, upstream = if (pShifted) 5 else 20, downstream = if (pShifted) 20 else 5, acceptedLengths = NULL, zeroPosition = upstream, scoring = "transcriptNormalized")
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 |
any type of reads, usualy ribo seq. As GAlignment, GRanges or GRangesList object. |
pShifted |
a logical (TRUE), are riboseq reads p-shifted to size 1 width reads? If upstream or downstream is set, this argument is irrelevant. |
upstream |
an integer (5), relative region to get upstream from. |
downstream |
an integer (20), relative region to get downstream from |
acceptedLengths |
an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted. |
zeroPosition |
an integer DEFAULT (upstream), the point if all windows are equal size, that should be set to position 0. 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), one of (zscore, transcriptNormalized, mean, median, sum, sumLength, fracPos), see ?coverageScorings. Use to choose meta coverage or per transcript. |
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 from to find upstream from. Unless upstream is negative, that is, going downstream.
a data.frame with lengths by coverage / vector of proportions
Other coverage: coverageScorings
,
metaWindow
,
scaledWindowPositions