summarizeSigCounts: Function summarizeSigCounts

Description Usage Arguments Details Value Author(s) Examples

View source: R/summarizeSigCounts.R

Description

Takes a contrast list produced by runContrasts. Also, specify columns to summarize and thresholds for each column. Optionally, provide a fold change threshold. Queries the topTable results and returns a dataframe with the summary results; gene counts that meet the specified conditions.

Usage

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summarizeSigCounts(
  ContrastList,
  columns = c("P.Value", "adj.P.Val", "Qvalue", "qvalue.lfdr", "ihw.adj_pvalue"),
  sigThresholds = c(0.01, 0.1, 0.1, 0.1, 0.1),
  fcThreshold = 0
)

Arguments

ContrastList

A list of topTable dataframes

columns

Vector of column names to summarize from topTable dataframes Default = c("P.Value", "adj.P.Val", "Qvalue", "qvalue.lfdr", "ihw.adj_pvalue")

sigThresholds

Thresholds to use for each column specified in columns Must be same length at columns argument. Default = c(0.01, 0.1, 0.1, 0.1, 0.1)

fcThreshold

fold-change threshold (absolute value, not logged)

Details

Specified column names that don't exist will be ignored. So normally, the defaults cover all the pvalue and FDR related columns and you'll only have to add a fcThreshold if you want one or modify the pvalue/fdr thresholds if you want different thresholds from the defaults.

Value

data.frame with one summary row per contrast

Author(s)

John Thompson, john.thompson@bms.com

Examples

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#get a contrast list from a dgeObj
MyContrastList <- getType(dgeObj, "topTable")

#all default thresholds, no fold change threshold
MySigSummary <- summarizeSigCounts (MyContrastList)

#all defaults with a foldchange threshold
MySigSummary <- summarizeSigCounts (MyContrastList, fcThreshold=1.5)

#change the pvalue and fdr thresholds
MySigSummary <- summarizeSigCounts (MyContrastList,
    sigThresholds = c(0.05, 0.2, 0.2, 0.2, 0.2))

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.