Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/ProteinGroup-class.R
The Exponentially Modified Protein Abundance Index (emPAI) is a label free quantitative measure of protein abundance based on protein coverage by peptide matches. The original publication is Ishihama Y, et al., Proteomics (2005).
1 2 3 4 5 6 7 | calculate.emPAI(protein.group, protein.g = reporterProteins(protein.group), normalize = FALSE,
observed.pep = c("pep", "mod.charge.pep"), use.mw = FALSE, combine.f = mean,
..., nmc = 0, report.all = FALSE)
n.observable.peptides(...)
observable.peptides(seq, nmc = 1, min.length = 6, min.mass = 600, max.mass = 4000,
custom = list(code = c("B", "Z", "J", "U"),
mass = c(164.554862, 278.61037, 213.12392, 150.953636)), ...)
|
protein.group |
ProteinGroup object. Its |
protein.g |
Protein group identifiers. |
normalize |
Normalize to sum = 1?. |
observed.pep |
What counts as observed peptide? |
report.all |
TOADD |
use.mw |
Use MW to normalize for protein size |
combine.f |
How to handle proteins seen only with shared peptides? |
seq |
Protein sequence. |
nmc |
Number of missed cleavages. |
min.length |
Minimum length of peptide. |
min.mass |
Minimum mass of peptide. |
max.mass |
Maximum mass of peptide. |
custom |
User defined residue for |
... |
Further arguments to |
The formula is
emPAI = 10^(N_observed/N_observable) -1
N_observed is the number of observed peptides - we use the count
of unique peptide without consideration of charge state.
N_observable is the number of observable peptides.
Sequence cleavage is done using Digest
.
Named numeric vector of emPAI values.
Florian P Breitwieser
Ishihama Y, et al., Proteomics (2005)
Digest
,
proteinInfo
,
getProteinInfoFromUniprot
,
calculate.dNSAF
,
ProteinGroup
1 2 3 | data(ibspiked_set1)
protein.group <- proteinGroup(ibspiked_set1)
calculate.emPAI(protein.group,protein.g=protein.g(protein.group,"CERU"))
|
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