compare: compare the peptide quantities in two experiments

In TeamMacLean/pepdiff: Analysing TSL PRM Peptide Data

compare the peptide quantities in two experiments

Description

For each peptide this function carries out the selected tests to determine peptides that are differentially abundant in the two experiments specified. Before tests are performed the technical replicates are merged and lowest observed value replacement for each missing biological replicate is done. All comparisins are performed as 'treatment / control'

Usage

compare(
  df,
  iters = 1000,
  treatment = NA,
  t_seconds = NA,
  control = NA,
  c_seconds = NA,
  tests = c("bootstrap_t")
)

Arguments

df	dataframe. Typically from 'import_data()'
iters	number of iterations to perform for iterative tests
treatment	name of the experimental treatment to use as the 'treatment' condition
t_seconds	time point of the 'treatment' condition to use
control	name of the experimental treatment to use as the 'control' condition
c_seconds	time point of the 'control' condition to use
tests	character vector of tests to use, one or more of: 'norm_quantile', 'bootstrap_t', 'wilcoxon', 'kruskal-wallis', 'rank_product'

Value

dataframe with original and replaced quantification values, natural fold change, biological replicates and p-value / fdr for each

TeamMacLean/pepdiff documentation built on April 24, 2023, 7:48 a.m.