write_dge: Write top table results to file.
In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description Usage Arguments Value See Also Examples

This is a convenience function for writing multiple top tables to files. It takes a list of top tables and corresponding file names and writes each table to that file.

1	write_dge(x, filename)

`x`	A list of top tables
`filename`	A character vector of same length as `x` containing filenames corresponding to each element in `x`.

It returns a NULL value if writing file to disk completes successfully.

rnaseq gather_counts show_counts limma_dge edger_dge construct_design construct_contrasts as.dgelist as.eset volcano_plot

path = system.file("tests", package="ganalyse")

# ----- raw ----- # 
raw_path = file.path(path, "raw", "annotation.txt")
raw_obj = rnaseq(raw_path, format="raw", experiment="sample")
raw_counts = gather_counts(raw_obj, by="gene-id", threshold=1L)
raw_design = construct_design(raw_counts, ~ 0 + condition)
raw_contrasts = construct_contrasts(
                     design = raw_design, 
                     treatA.vs.control = conditiontreatA-conditioncontrol, 
                     treatB.vs.control = conditiontreatB-conditioncontrol
                 )
# DE genes between treatA and control
ans = edger_dge(raw_counts, design=raw_design, 
             contrast=raw_contrasts[, "treatA.vs.control"])
## Not run: 
write_dge(ans, "treatA_vs_control.tsv")

## End(Not run)