getShiftingPromoters: Select consensus clusters with shifting score above threshold

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

Select consensus clusters with shifting score above threshold

Description

Extracts consensus clusters with shifting score and/or FDR (adjusted P-value from Kolmogorov-Smirnov test) above specified threshold. Returns their genomic coordinates, total CAGE signal and the position of dominant TSS in the two compared groups of CAGE samples, along with the value of the shifting score, P-value and FDR. Scores and P-values/FDR have to be calculated beforehand by calling scoreShift function.

Usage

getShiftingPromoters(
  object,
  groupX,
  groupY,
  tpmThreshold = 0,
  scoreThreshold = -Inf,
  fdrThreshold = 1
)

## S4 method for signature 'CAGEexp'
getShiftingPromoters(
  object,
  groupX,
  groupY,
  tpmThreshold = 0,
  scoreThreshold = -Inf,
  fdrThreshold = 1
)

Arguments

object	A CAGEexp object.
groupX, groupY	Character vector of the one or more CAGE dataset labels in the first (groupX) and in the second group (groupY). Shifting promoters for the specified group pair are returned.
tpmThreshold	Consensus clusters with total CAGE signal >= tpmThreshold in each of the compared groups will be returned.
scoreThreshold	Consensus clusters with shifting score >= scoreThreshold will be returned. The default value -Inf returns all consensus clusters (for which score could be calculated, i.e. the ones that have at least one tag in each of the compared samples).
fdrThreshold	Consensus clusters with adjusted P-value (FDR) from Kolmogorov-Smirnov test >= fdrThreshold will be returned. The default value 1 returns all consensus clusters (for which K-S test could be performed, i.e. the ones that have at least one tag in each of the compared samples).

Value

Returns a data.frame of shifting promoters with genomic coordinates and positions of dominant TSS and CAGE signal in the two compared (groups of) samples, along with shifting score and adjusted P-value (FDR).

Author(s)

Vanja Haberle

Sarvesh Nikumbh

See Also

Other CAGEr promoter shift functions: scoreShift()

Examples

getShiftingPromoters( exampleCAGEexp
                    , groupX = "Zf.unfertilized.egg"
                    , groupY = "Zf.30p.dome") |> head()

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