DE.edgeR.RdPerform DEA by EdgeR on normalized dataset or dataset with adjusting factor. The normalized data can be provided as normalized counts or by adjusting factor for the original count data.
DE.edgeR(RC, groups, Pval = 0.01, normalized = TRUE, adjust = NULL)| RC | data in the format of data frame or matrix, with columns for samples and raws for genes. |
|---|---|
| groups | vector of characters indicating the group for each sample. |
| Pval | cut-off point for p-values to identify DE genes. |
| normalized | Logical, whether the data is provided as normalized counts.
If set to FALSE, adjustment factors must be provided using the |
| adjust | Adjusting factors for normalizing the count data. Must be
provided if the data is not normalized beforehand as indicated by the
|
list, containing id.list (names of DE genes), p.val, and log2.FC.
https://ucdavis-bioinformatics-training.github.io/2018-June-RNA-Seq-Workshop/thursday/DE.html
edgeR.benchmark <- DE.edgeR(data.benchmark, data.group)
str(edgeR.benchmark)
#> List of 3
#> $ id.list: chr [1:71] "hsa-miR-183" "hsa-miR-182" "hsa-miR-129-2-3p" "hsa-miR-96" ...
#> $ p.val : num [1:1033] 2.53e-10 4.34e-10 1.42e-07 2.58e-07 7.56e-07 ...
#> $ log2.FC: num [1:1033] 3.9 3.45 4.28 3.08 1.82 ...