peptide.count {isobar} | R Documentation |
Report the peptide count, spectral count and sequence coverage for supplied proteins.
peptide.count(protein.group, protein.g = reporterProteins(protein.group), specificity = c("reporter-specific", "group-specific", "unspecific"), ...) spectra.count(protein.group, protein.g = reporterProteins(protein.group), specificity = c("reporter-specific", "group-specific", "unspecific"), modif = NULL, ...) sequence.coverage(protein.group, protein.g = reporterProteins(protein.group), specificity = c("reporter-specific", "group-specific", "unspecific"), simplify = TRUE, ...)
protein.group |
ProteinGroup object. |
protein.g |
Protein group identifier. |
specificity |
Specificity of peptides. |
modif |
Only count peptides having a certain modification. |
simplify |
If simplify=TRUE, a named numeric vector is returned, with the mean sequence coverage of the ACs of each protein.g supplied. Else, a list with the length of protein.g is returned having the sequence coverage for each protein AC. |
... |
Further arguments to |
Florian P Breitwieser
calculate.emPAI
,
calculate.dNSAF
,
ProteinGroup
data(ibspiked_set1) sc <- spectra.count(proteinGroup(ibspiked_set1)) pc <- peptide.count(proteinGroup(ibspiked_set1)) plot(jitter(sc),jitter(pc),log="xy")