detectedTxInfo: Summarize detected transcript results

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Summarize detected transcript results

Description

Summarize detected transcript results

Usage

detectedTxInfo(
  detectedTxL,
  Gene = NULL,
  Tx = NULL,
  Groups = NULL,
  detectedOnly = NULL,
  ...
)

Arguments

detectedTxL	list output from defineDetectedTx()
Gene	optional character vector of one or more genes of interest, used to find transcript_id entries in the detectedTxL input data. If not supplied, Tx is expected.
Tx	optional character vector used to subset summary data, usually intended to keep rows in a specific order for a given set of transcripts.
Groups	optional character vector used to subset the groups (colnames) returned for each data.frame.
detectedOnly	NULL or logical indicating whether to restrict Tx to detected transcripts, defined by detectedTxL$detectedTx. When: * `detectedOnly=NULL` then `Tx` is used as-is. * `detectedOnly=TRUE` and `Tx=NULL` then `Tx` uses all detected transcripts from `detectedTxL$detectedTx`. * `detectedOnly=TRUE` and `Tx` is supplied, it is restricted to detected transcripts from `detectedTxL$detectedTx`. * `detectedOnly=FALSE` and `Tx=NULL` then `Tx` uses all transcripts. * `detectedOnly=FALSE` and `Tx` is supplied, it is used as-is.
...	additional arguments are ignored.

Details

This function provides a simple summary of the results of defineDetectedTx(), typically for a given gene of interest.

By default, either Gene or Tx must be supplied, however to return data for all genes, use either detectedOnly=TRUE to return data only for detected transcripts, or detectedOnly=FALSE to return all data including transcripts that are not determined to be detected.

Value

list of data.frame objects, each containing one summary table of data used to support whether each transcript were called "detected."

See Also

Other jam RNA-seq functions: assignGRLexonNames(), closestExonToJunctions(), combineGRcoverage(), defineDetectedTx(), exoncov2polygon(), flattenExonsBy(), getGRcoverageFromBw(), groups2contrasts(), internal_junc_score(), makeTx2geneFromGtf(), make_ref2compressed(), prepareSashimi(), runDiffSplice(), sortSamples(), spliceGR2junctionDF()

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.