View source: R/qc_proteome_coverage.R
qc_proteome_coverage | R Documentation |
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.
qc_proteome_coverage( data, sample, protein_id, organism_id, reviewed = TRUE, plot = TRUE, interactive = FALSE )
data |
a data frame that contains at least sample names and protein ID's. |
sample |
a character column in the |
protein_id |
a character or numeric column in the |
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). |
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.
# 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 )
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