miscGlobal: Detect global shape variants in RNA-seq inputData

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

Detect global shape variants in RNA-seq inputData

Description

This function discovers outlying subjects whose RNA-seq have abnormal shapes and provides the most outlying direction for each outlier.

Usage

miscGlobal(
  inputData,
  siglev = 1e-04,
  ADcutoff = 3,
  PCnum = NULL,
  maxPCnum = 10,
  reducedReturn = TRUE
)

Arguments

inputData	precessed RNA-seq data from process_data
siglev	the significance level of the Chi-squared distribution. Default is 1e-10.
ADcutoff	a cutoff value for checking the normality based on Anderson-Darling test statistic
PCnum	the number of PCs to be used. If NULL (the default) the number of PCs will be estimated.
maxPCnum	the maximum number of PCs to be used. Default is 20.
reducedReturn	logical, whether to show less results and not to return large matrices. Default is TRUE.
subt.mean	logical, whether to subtract mean before SVD. Default is FALSE.

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