autoGO (version 1.0.1)

filtering_DE: Filtering DESeq2 results

Description

We could be in a position to carry out multiple filters on the results of the differential analysis, in order not to repeat all the deseq_analysis.R code which provides for the actual computation of the differential analysis, the filtering_DE.R function has been implemented to be able to filter the file(s) " * _allres.tsv " and generate all the folders and files associated with the specific filters applied.

The function automatically searches inside the folders where_results and outfolder the file(s) (See ?deseq_analysis()) "_allres.tsv" and generates folders and files in the same folders with the new filters for foldchange and pvalue respectively.

Usage

filtering_DE(
  padj_threshold = 0.05,
  log2FC_threshold = 1,
  outfolder = "./results",
  save_excel = FALSE
)

Value

No return value. Files will be produced as part of normal execution.

Arguments

padj_threshold

(Default = 0.05) Threshold value for adjusted p-value filtering.

log2FC_threshold

(Default = 0) Threshold value for log2(Fold Change) filtering.

outfolder

(Default = "./results") Name of the folder in which the new output is written.

save_excel

(Default = FALSE) Write output in MS Excel file format (.xlsx).

Examples

if (FALSE) {
filtering_DE(
  padj_threshold = 0.05,
  log2FC_threshold = 1,
  outfolder = "./results",
  save_excel = F
)
}