plasma_contamination: plasma_contamination

In saezlab/plasmaContamination: plasma proteomic quality control

plasma_contamination

Description

This function performs an enrichment analysis to test whether a given proteomic sample is contaminated with markers from erythrocyte, platelets or coagulation. The signatures are taken from: https://www.sciencedirect.com/science/article/pii/S2405471216300722

Usage

plasma_contamination(
  df,
  n_perm = 1000,
  plot = T,
  verbose = T,
  signatures = NULL,
  manual_colors = NULL
)

Arguments

df	as data frame with row names as gene symbols, and then each column should be a sample or the t-values of a differential analysis

Value

a data frame with normalized enrichment (mean) scores for the contamination signatures. The higher the score, the higher the potential contamination

Examples

library(plasmaContamination)
data(test_data)

conta_scores <- plasma_contamination(test_data)

saezlab/plasmaContamination documentation built on Jan. 4, 2023, 3:04 a.m.