ComputePSI.RI {MARVEL}

Compute retained-intron (RI) percent spliced-in (PSI) values

Description

Validate RI splicing events and subsequently computes percent spliced-in (PSI) values these high-quality splicing events.

Usage

ComputePSI.RI(
  MarvelObject,
  CoverageThreshold,
  IntronCounts,
  thread,
  read.length = 1
)

Arguments

MarvelObject

Marvel object. S3 object generated from CreateMarvelObject function.

CoverageThreshold

Numeric value. Coverage threshold below which the PSI of the splicing event will be censored, i.e. annotated as missing (NA). Coverage defined as the total number of reads supporting both included and excluded isoforms.

IntronCounts

Data frame. Columns indicate sample IDs, rows indicate intron coordinates, and values indicate total intron coverage. The first column needs to be named coord.intron. These values will be combined with splice junction counts in the MARVEL object to compute PSI values.

thread

Numeric value. Set number of threads.

read.length

Numeric value. The length of read. This number will be specific to the sequencing mode. E.g. read length should be set to 150 when samples were sequenced in 150bp paired-end or single-end. This option should only be specified when users used read-counting approach for computing intron counts. The option should be left with its default value 1 when users tabulated the per-base count and summed them up to arrive at the intron counts.

Value

An object of class S3 with new slots $SpliceFeatureValidated$RI and $PSI$RI.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

marvel.demo <- ComputePSI.RI(MarvelObject=marvel.demo,
                             CoverageThreshold=10,
                             IntronCounts=marvel.demo$IntronCounts,
                             thread=1
                             )