artmsResultsWide {artMS} | R Documentation

## Reshape the MSstats results file from long to wide format

### Description

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.

### Usage

    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")

[Package artMS version 1.4.3 Index]