degResults {DEGreport} | R Documentation |
Complete report from DESeq2 analysis
degResults(res = NULL, dds, rlogMat = NULL, name, org = NULL, FDR = 0.05, do_go = FALSE, FC = 0.1, group = "condition", xs = "time", path_results = ".", contrast = NULL)
res |
output from |
dds |
|
rlogMat |
matrix from |
name |
string to identify results |
org |
an organism annotation object, like org.Mm.eg.db. NULL if you want to skip this step. |
FDR |
int cutoff for false discovery rate. |
do_go |
boolean if GO enrichment is done. |
FC |
int cutoff for log2 fold change. |
group |
string column name in colData(dds) that separates samples in meaninful groups. |
xs |
string column name in colData(dss) that will be used as X axes in plots (i.e time) |
path_results |
character path where files are stored. NULL if you don't want to save any file. |
contrast |
list with character vector indicating the fold change values from different comparisons to add to the output table. |
ggplot2 object
data(humanGender) library(DESeq2) idx <- c(1:10, 75:85) dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx], colData(humanGender)[idx,], design=~group) dse <- DESeq(dse) res <- degResults(dds = dse, name = "test", org = NULL, do_go = FALSE, group = "group", xs = "group", path_results = NULL)