Identify differentially expressed proteins between groupsSource:
This function performs differential expression analysis on protein intensity data with limma.
find_dep( df, save_output = FALSE, save_tophits = FALSE, file_path = NULL, adj_method = "BH", cutoff = 0.05, lfc = 1, n_top = 20 )
norm_dfobject or an
TRUEsaves results from the differential expression analysis in a text file labeled "limma_output.txt" in the directory specified by
n_topnumber of top hits from the differential expression analysis in a text file labeled "TopHits.txt" in the directory specified by
A string containing the directory path to save the file.
Method used for adjusting the p-values for multiple testing. Default is
"BH"for "Benjamini-Hochberg" method.
Cutoff value for p-values and adjusted p-values. Default is 0.05.
Minimum absolute log2-fold change to use as threshold for differential expression.
The number of top differentially expressed proteins to save in the "TopHits.txt" file. Default is
save_outputsaves the complete results table from the differential expression analysis.
save_tophitsfirst subsets the results to those with absolute log fold change of more than 1, performs multiple correction with the method specified in
adj_methodand outputs the top
n_topresults based on lowest p-value and adjusted p-value.
If the number of hits with absolute log fold change of more than 1 is less than
find_depprints only those with log-fold change > 1 to "TopHits.txt".
file_pathis not specified, text files will be saved in a temporary directory.
Ritchie, Matthew E., et al. "limma powers differential expression analyses for RNA-sequencing and microarray studies." Nucleic acids research 43.7 (2015): e47-e47.
## Perform differential expression analysis using default settings fit_df1 <- find_dep(ecoli_norm_df) #> Warning: 3 very small variances detected, have been offset away from zero #> 1186 siginificantly differentially expressed proteins found. ## Change p-value and adjusted p-value cutoff fit_df2 <- find_dep(ecoli_norm_df, cutoff = 0.1) #> Warning: 3 very small variances detected, have been offset away from zero #> 1227 siginificantly differentially expressed proteins found.