Count the number of features (rows) per protein

For differential testing with https://www.bioconductor.org/packages/release/bioc/html/DEqMS.htmlDEqMS, one needs to identify the number of features, e.g PSMs or peptides per protein. This function returns the number of features per protein per sample.

count_features_per_protein(obj, master_prot_col = "Master.Protein.Accessions")

Arguments

obj

MSnSet. Contains PSMs or peptides.

master_prot_col

character Column name for master protein ID

Value

tibble with feature counts per sample per protein.

Examples

# Use a small example TMT dataset included with the camprotR package
df <- psm_tmt_total

# Make an MSnSet
df_exprs <- as.matrix(df[, grep("Abundance", colnames(df))])
colnames(df_exprs) <- gsub("Abundance\\.", "", colnames(df_exprs))

df_fData <- df[, grep("Abundance", colnames(df), invert = TRUE)]

psm <- MSnbase::MSnSet(exprs = df_exprs, fData = df_fData)

# Count the number of PSMs per protein
count_features_per_protein(psm, master_prot_col = "Master.Protein.Accessions")
#> # A tibble: 23,542 × 3
#> # Groups:   sample [10]
#>    sample Master.Protein.Accessions     n
#>    <chr>  <chr>                     <int>
#>  1 126    ""                            2
#>  2 126    "A0AVT1"                      1
#>  3 126    "A0PJZ3"                      1
#>  4 126    "A0PK00"                      1
#>  5 126    "A1L020"                      1
#>  6 126    "A1L0T0"                      4
#>  7 126    "A1L390"                      1
#>  8 126    "A1X283"                      1
#>  9 126    "A3KMH1"                      1
#> 10 126    "A3KN83"                      1
#> # ℹ 23,532 more rows