Proteome coverage per sample and total

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
)

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

# \donttest{
# 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
)
#> # A tibble: 8 × 3
#>   sample type                percentage
#>   <fct>  <fct>                    <dbl>
#> 1 A      proteins_detected         2.21
#> 2 A      proteins_undetected      97.8 
#> 3 B      proteins_detected        22.1 
#> 4 B      proteins_undetected      77.9 
#> 5 C      proteins_detected        22.1 
#> 6 C      proteins_undetected      77.9 
#> 7 Total  proteins_detected        44.2 
#> 8 Total  proteins_undetected      55.8 

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

# }