flagLowExpCTSS: Flag CTSSes based on sample expression

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Flag CTSSes based on sample expression

Description

Flag CTSSes for that do not pass an expression threshold in at least a given number of samples. This is typically used to ignore CTSSes that have been seen only once in a single sample, as they can be considered to not be reproduced.

Usage

flagLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

## S4 method for signature 'CAGEr'
flagLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

## S4 method for signature 'RangedSummarizedExperiment'
flagLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

## S4 method for signature 'DataFrame'
flagLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

## S4 method for signature 'matrix'
flagLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

filterLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

## S4 method for signature 'CAGEr'
filterLowExpCTSS(
  object,
  threshold = 1,
  nrPassThreshold = 1,
  thresholdIsTpm = TRUE
)

Arguments

object	An object from the CAGEr package that contains expression values for multiple samples.
threshold	Flag CTSSs with signal ⁠< threshold⁠.
nrPassThreshold	Only flag CTSSs when signal is below threshold in at least nrPassThreshold samples.
thresholdIsTpm	Logical, is threshold raw tag count value (FALSE) or normalized signal (TRUE).

Value

flagLowExpCTSS returns a Rle vector where TRUE indicates the index of a CTSS that passes the filter.

filterLowExpCTSS returns the CAGEr object where the output of flagLowExpCTSS was stored internally.

See Also

Other CAGEr filter functions: filteredCTSSidx(), flagByUpstreamSequences()

Examples

flagLowExpCTSS(exampleCAGEexp, threshold = 100, nrPassThreshold = 2)

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.