detectTranscripts: detectTranscripts detects transcripts de novo using a...
In coregenomics/groHMM: GRO-seq Analysis Pipeline

Description Usage Arguments Details Value Author(s) Examples

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.

1 2	detectTranscripts(reads = NULL, Fp = NULL, Fm = NULL, LtProbA = -5, LtProbB = -200, UTS = 5, size = 50, threshold = 0.1)

`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`	Variance 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.

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, transParams, 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

library(GenomicAlignments)
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