qc_contaminants: Percentage of contaminants per sample

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Percentage of contaminants per sample

Description

Calculates the percentage of contaminating proteins as the share of total intensity.

Usage

qc_contaminants(
  data,
  sample,
  protein,
  is_contaminant,
  intensity,
  n_contaminants = 5,
  plot = TRUE,
  interactive = FALSE
)

Arguments

data	a data frame that contains at least the input variables.
sample	a character or factor column in the data data frame that contains the sample names.
protein	a character column in the data data frame that contains protein IDs or protein names.
is_contaminant	a logical column that indicates if the protein is a contaminant.
intensity	a numeric column in the data data frame that contains the corresponding raw or normalised intensity values (not log2).
n_contaminants	a numeric value that indicates how many contaminants should be displayed individually. The rest is combined to a group called "other". The default is 5.
plot	a logical value that indicates if a plot is returned. If FALSE a table is returned.
interactive	a logical value that indicates if the plot is made interactive using the r package plotly.

Value

A bar plot that displays the percentage of contaminating proteins over all samples. If plot = FALSE a data frame is returned.

Examples

data <- data.frame(
  sample = c(rep("sample_1", 10), rep("sample_2", 10)),
  leading_razor_protein = c(rep(c("P1", "P1", "P1", "P2", "P2", "P2", "P2", "P3", "P3", "P3"), 2)),
  potential_contaminant = c(rep(c(rep(TRUE, 7), rep(FALSE, 3)), 2)),
  intensity = c(rep(1, 2), rep(4, 4), rep(6, 4), rep(2, 3), rep(3, 5), rep(4, 2))
)

qc_contaminants(
  data,
  sample = sample,
  protein = leading_razor_protein,
  is_contaminant = potential_contaminant,
  intensity = intensity
)

protti documentation built on Oct. 22, 2024, 1:06 a.m.