degSummary {DEGreport} | R Documentation |
Print Summary Statistics of Alpha Level Cutoffs
degSummary( object, alpha = c(0.1, 0.05, 0.01), contrast = NULL, caption = "", kable = FALSE )
object |
Can be DEGSet or DESeqDataSet or DESeqResults. |
alpha |
Numeric vector of desired alpha cutoffs. |
contrast |
Character vector to use with |
caption |
Character vector to add as caption to the table. |
kable |
Whether return a |
Lorena Pantano
original idea of multiple alpha values and code syntax from Michael Steinbaugh.
library(DESeq2) data(humanGender) idx <- c(1:5, 75:80) counts <- assays(humanGender)[[1]] dse <- DESeqDataSetFromMatrix(counts[1:1000, idx], colData(humanGender)[idx,], design = ~group) dse <- DESeq(dse) res1 <- results(dse) res2 <- degComps(dse, contrast = c("group_Male_vs_Female")) degSummary(dse, contrast = "group_Male_vs_Female") degSummary(res1) degSummary(res1, kable = TRUE) degSummary(res2[[1]])