grandR (version 0.2.6)

GetSignificantGenes: Significant genes

Description

Return significant genes for this grandR object

Usage

GetSignificantGenes(
  data,
  analysis = NULL,
  regex = TRUE,
  criteria = NULL,
  as.table = FALSE,
  use.symbols = TRUE,
  gene.info = TRUE
)

Value

a vector of gene names (or symbols), or a table

Arguments

data

the grandR object

analysis

the analysis to use, can be more than one and can be regexes (see details)

regex

interpret analyses as regex?

criteria

the criteria used to define what significant means; if NULL, Q<0.05 & abs(LFC)>=1 is used; can use the column names of the analysis table as variables, should be a logical or numerical value per gene (see Details)

as.table

return a table

use.symbols

return them as symbols (gene ids otherwise)

gene.info

add gene infos to the output table

Details

The analysis parameter (just like for GetAnalysisTable can be a regex (that will be matched against all available analysis names). It can also be a vector (of regexes). Be careful with this, if more than one table e.g. with column LFC ends up in here, only the first is used (if criteria=LFC).

The criteria parameter can be used to define how analyses are performed. If criteria is a logical, it obtains significant genes defined by cut-offs (e.g. on q value and LFC). If it is a numerical, all genes are returned sorted (descendingly) by this value. The columns of the given analysis table(s) can be used to build this expression.

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c(Design$Condition,Design$dur.4sU,Design$Replicate))
sars <- subset(sars,Coldata(sars,Design$dur.4sU)==2)
sars<-LFC(sars,mode="total",contrasts=GetContrasts(sars,contrast=c("Condition","Mock")))
GetSignificantGenes(sars,criteria=LFC>1)