qc_proteome_coverage {protti} | R Documentation |
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 |
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). |
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
)