Scissor: This function is a wrapper of the necessary functions to...

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

This function is a wrapper of the necessary functions to detect RNA-seq shape changes at a single gene in a single command.

Description

This function is a wrapper of the necessary functions to detect RNA-seq shape changes at a single gene in a single command.

Usage

Scissor(
  pileupData,
  Ranges,
  siglev = 1e-04,
  logshiftVal = NULL,
  windowSize = 50,
  plotNormalization = TRUE,
  reducedReturn = FALSE
)

Arguments

pileupData	a pile-up data matrix obtained from bam files, i.e. base-level raw counts. Columns are samples and rows are genomic positions.
Ranges	a list of information for genomic regions. get_Ranges.
siglev	a significance level for detecting outliers. Default is 1e-4.
logshiftVal	a pseudo count added to raw counts before the logarithmic transformation. Default is NULL and automatically selects the pseudo count based on the implemented algorithm.
windowSize	a window size used in the local shape change detection.
plotNormalization	logical, whether to plot variation with respect to overall expression with fitted curve. Default is FALSE
reducedReturn

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.