getTxDensity {groHMM} | R Documentation |
Calculates transcript density for transcripts which overlapps with annotations. For 'run genes together' or 'broken up a single annotation' errors, best overlapped transcripts or annotations are used.
getTxDensity(tx, annox, plot = TRUE, scale = 1000L, nSampling = 0L, samplingRatio = 0.1, ...)
tx |
GRanges of transcripts. |
annox |
GRanges of non-overlapping annotatoins. |
plot |
Logical. If TRUE, plot transcript density. Default: TRUE |
scale |
Numeric. Scaled size of a gene for transcript density calculation. Default: 1000L |
nSampling |
Numeric. Number of subsampling. Default: 0L |
samplingRatio |
Numeric. Ratio of sampling for annotations. Default: 0.1 |
... |
Extra argument passed to mclapply. |
Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors set the option 'mc.cores'.
Returns a list of FTD, TTD, PostTTS, and AUC.
Minho Chae
tx <- GRanges("chr7", IRanges(start=seq(1000,4000, by=1000), width=seq(1000, 1300, by=100)), strand=rep("+", 4)) annox <- GRanges("chr7", IRanges(start=seq(1100,4100, by=1000), width=seq(900, 1200, by=100)), strand=rep("+", 4)) ## Not run: # density <- getTxDensity(tx, annox)