qc_proteome_coverage: Proteome coverage per sample and total

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

Proteome coverage per sample and total

Description

Calculates the proteome coverage for each samples and for all samples combined. In other words t he fraction of detected proteins to all proteins in the proteome is calculated.

Usage

qc_proteome_coverage(
  data,
  sample,
  protein_id,
  organism_id,
  reviewed = TRUE,
  plot = TRUE,
  interactive = FALSE
)

Arguments

data	a data frame that contains at least sample names and protein ID's.
sample	a character column in the data data frame that contains the sample name.
protein_id	a character or numeric column in the data data frame that contains protein identifiers such as UniProt accessions.
organism_id	a numeric value that specifies a NCBI taxonomy identifier (TaxId) of the organism used. Human: 9606, S. cerevisiae: 559292, E. coli: 83333.
reviewed	a logical value that determines if only reviewed protein entries will be considered as the full proteome. Default is TRUE.
plot	a logical value that specifies whether the result should be plotted.
interactive	a logical value that indicates whether the plot should be interactive (default is FALSE).

Value

A bar plot showing the percentage of of the proteome detected and undetected in total and for each sample. If plot = FALSE a data frame containing the numbers is returned.

Examples

# Create example data
proteome <- data.frame(id = 1:4518)
data <- data.frame(
  sample = c(rep("A", 101), rep("B", 1000), rep("C", 1000)),
  protein_id = c(proteome$id[1:100], proteome$id[1:1000], proteome$id[1000:2000])
)

# Calculate proteome coverage
qc_proteome_coverage(
  data = data,
  sample = sample,
  protein_id = protein_id,
  organism_id = 83333,
  plot = FALSE
)

# Plot proteome coverage
qc_proteome_coverage(
  data = data,
  sample = sample,
  protein_id = protein_id,
  organism_id = 83333,
  plot = TRUE
)

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