metaWindow {ORFik} | R Documentation |
Sums up coverage over set of GRanges objects as a meta representation.
metaWindow(x, windows, scoring = "sum", withFrames = FALSE, zeroPosition = NULL, scaleTo = 100, returnAs = "data.frame", fraction = NULL, feature = NULL, forceUniqueEven = !is.null(scoring))
x |
GRangesList/GRanges object of your reads. Remember to resize them beforehand to width of 1 to focus on 5' ends of footprints, if that is wanted. |
windows |
GRangesList or GRanges of your ranges |
scoring |
a character, one of (zscore, transcriptNormalized, mean, median, sum, sumLength, NULL), see ?coverageScorings |
withFrames |
a logical (TRUE), return positions with the 3 frames, relative to zeroPosition. zeroPosition is frame 0. |
zeroPosition |
an integer DEFAULT (NULL), 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. |
scaleTo |
an integer (100), if windows have different size, a meta window can not directly be created, since a meta window must have equal size for all windows. Rescale all windows to scaleTo. i.e c(1,2,3) -> size 2 -> c(1, sum(2,3)) etc. |
returnAs |
a character (data.frame), do data.table for speed. |
fraction |
a character/integer (NULL), the fraction i.e (27) for read length 27, or ("LSU") for large sub-unit TCP-seq. |
feature |
a character string, info on region. Usually either gene name, transcript part like cds, leader, or CpG motifs etc. |
forceUniqueEven, |
a logical (TRUE), require that all windows are of same width and even. To avoid bugs. |
A data.frame or data.table with scored counts (score) of reads mapped to positions (position) specified in windows along with frame (frame).
Other coverage: coverageScorings
,
scaledWindowPositions
,
windowPerReadLength
library(GenomicRanges) windows <- GRangesList(GRanges("chr1", IRanges(c(50, 100), c(80, 200)), "-")) x <- GenomicRanges::GRanges( seqnames = "chr1", ranges = IRanges::IRanges(c(100, 180), c(200, 300)), strand = "-") metaWindow(x, windows, withFrames = FALSE)