Description Usage Arguments Value Examples
Perform network module of pathway-based approach.
1 2 | perform_network_pathway(df_mut_score_wide, whole_fc_genes, expressed_genes,
mcutoff = 2, fraction = 0.6, padj = 0.01, log2_fold_change = 2)
|
df_mut_score_wide |
A dataframe. |
whole_fc_genes |
A list. |
expressed_genes |
A character vector. |
mcutoff |
A float number between 0 and 6, default is 2. |
fraction |
A float number between 0 and 1, default is 0.6. |
padj |
Adjusted p value threshold for differential analysis, default is 0.01. |
log2_fold_change |
log2 transformed fold change threshold for differential analysis, default is 2. |
A list.
1 2 3 4 5 6 7 | ## Not run:
prepare_ma()
res.gene <- perform_gene_pathway(hnsc_mut_part, hnsc_exp_part)
res.network <- perform_network_pathway(res.gene[[2]], res.gene[[3]], hnsc_expressed_genes)
## End(Not run)
|
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