marker.selection: Select circRNA markers To establish a possible impact of...

In ABuratin/CircTarget: Pipeline for study interaction and association between circular and linear RNA

Select circRNA markers To establish a possible impact of circRNA in gene expression we select a subset of circRNA defined as markers: only circRNA which expression can discretize two groups (DESeq adj. p-value<.01) have been selected.

Description

Select circRNA markers To establish a possible impact of circRNA in gene expression we select a subset of circRNA defined as markers: only circRNA which expression can discretize two groups (DESeq adj. p-value<.01) have been selected.

Usage

marker.selection(
  dat,
  dds,
  sf,
  p.cutoff = 0.01,
  lfc.cutoff = NULL,
  method.d,
  method.c,
  k,
  choose.k = FALSE,
  index.m = NULL,
  max.nc = 2,
  plot = FALSE,
  n = 9,
  median = TRUE
)

Arguments

dat	circRNA data set
dds	DeseqDataSet object filterd
sf	sizefactor
p.cutoff	select only circRNAs signficantly differentially expressed
lfc.cutoff	log fold change cutoff to select circRNAs highly deregulated
method.d	method for calculate matrix distance
method.c	method for clustering
k	number of group in K-means algorithm

Value

list of two elements: circRNAs estimate, circRNA-target ids

ABuratin/CircTarget documentation built on July 6, 2022, 9:06 a.m.