ListOfExpressedGenes: Give the list of expressed genes in a study in function of...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Give the list of expressed genes in a study in function of the selected type of comparison

Description

Give the list of expressed genes in a study in function of the selected type of comparison

Usage

ListOfExpressedGenes(DF, threshold = 0, out = "rownames",
  type = "gt", nb)

Arguments

DF	numeric data.frame
threshold	numeric, default: 0. Threshold above which a gene is considered as expressed
out	result format; 'rownames': names of the relevant genes 'data.frame': data.frame with the relevant genes 'df': alias of 'data.frame' 'index': indices of the rows of the relevant genes 'ind': alias of 'index'
type	type of comparison to be considered. 'gt': expression should be strictly greater than threshold. 'ge': expression should be greater than or equal to threshold. 'eq': expression should be equal to threshold. 'lt': expression should strictly be lesser than threshold 'le': expression should be lesser than or equal to threshold 'notDetected': No expression is detected above or at threshold 'ubi': expression is detected everywhere 'unique': expression is detected solely in one condition 'mixedH': expression is detected above threshold in 'nb' tissues 'mixedl': expression is detected below threshold in 'nb' tissues
nb	Number of tissues that one should be expressed to be considered for mixed expression

Value

several types of objects are available. Selection through "out"

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.