Description Usage Arguments Details Value Author(s) Examples
View source: R/summarizeSigCounts.R
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.
1 2 3 4 5 6 | 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
)
|
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) |
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.
data.frame with one summary row per contrast
John Thompson, john.thompson@bms.com
1 2 3 4 5 6 7 8 9 10 11 12 | #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))
|
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