detectTranscripts {groHMM} | R Documentation |
Read counts can be specified as either a GRanges object (reads), or using a fixed-step wiggle-format passed in a list (Fp and Fm). Either reads or BOTH Fp and Fm must be specified.
detectTranscripts(reads = NULL, Fp = NULL, Fm = NULL, LtProbA = -5, LtProbB = -200, UTS = 5, size = 50, threshold = 0.1, debug = TRUE, ...)
reads |
A GRanges object representing a set of mapped reads. |
Fp |
Wiggle-formatted read counts on "+" strand. Optionally, Fp and Fm represent list() filled with a vector of counts for each chromosome. Can detect transcripts starting from a fixed-step wiggle. |
Fm |
Wiggle-formatted read counts on "-" strand. |
LtProbA |
Log probability of t... . Default: -5. One of these is just an initialization, and the final value is set by EM. The other is a holdout parameter. |
LtProbB |
Log probability of t... . Default: -200. |
UTS |
Varience in read counts of the untranscribed sequence. Default: 5. |
size |
Log probability of t... . Default: -5. |
threshold |
Threshold change in total likelihood, below which EM exits. |
debug |
If set to TRUE, provides additional print options. Default: FALSE |
... |
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'.
Reference: Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 2011 May 13;145(4):622-34. doi: 10.1016/j.cell.2011.03.042.
Returns a list of emisParams, trnasParams, viterbiStates, and transcripts. The transcript element is a GRanges object representing the predicted genomic coordinates of transcripts on both the + and - strand.
Charles G. Danko and Minho Chae
S0mR1 <- as(readGAlignments(system.file("extdata", "S0mR1.bam", package="groHMM")), "GRanges") ## Not run: # hmmResult <- detectTranscripts(S0mR1, LtProbB=-200, UTS=5, threshold=1) # txHMM <- hmmResult$transcripts