Reshape the MSstats results file from long to wide format

Source: R/MSstats_functions.R

Converts the normal MSStats results.txt file into "wide" format where each row represents a unique protein's results, and each column represents the comparison made by MSStats. The fold change and p-value of each comparison will be its own column.

artmsResultsWide(
  results_msstats,
  output_file = NULL,
  select_pvalues = c("adjpvalue", "pvalue"),
  species,
  verbose = TRUE
)

Arguments

results_msstats

(char) Input file name and location (MSstats results.txt file)
output_file

(char) Output file name and location (e.g. results-wide.txt). If NULL (default) returns an R object (data.frame)
select_pvalues

(char) Either

  • pvalue or

  • adjpvalue (default)
species

(char) Specie name for annotation purposes. Check ?artmsMapUniprot2Entrez to find out more about the supported species (e.g species = "human")
verbose

(logical) TRUE (default) shows function messages

Value

(output file tab delimited) reshaped file with unique protein ids and as many columns log2fc and adj.pvalues as comparisons available

Examples

ph_results_wide <- artmsResultsWide(
                         results_msstats = artms_data_ph_msstats_results,
                         output_file = NULL,
                         species = "human")

#> >> RESHAPING MSSTATS RESULTS TO wide FORMAT