PropertyofPepSingle: Title Properties of whole peptides
In yujijun/neoantigenML: Machine Learning Methods for Neoantigen Filtering

PropertyofPepSingle

R Documentation

Title Properties of whole peptides

Description

Title Properties of whole peptides

Usage

PropertyofPepSingle(
  peptides,
  PropAll = c("aaComp", "aIndex", "autoCorrelation", "autoCovariance", "blosumIndices",
    "boman", "charge", "crossCovariance", "crucianiProperties", "fasgaiVectors",
    "hmoment", "hydrophobicity", "instaIndex", "kideraFactors", "mswhimScores", "mw",
    "mz", "pl", "protFP", "stScales", "tScales", "vhseScales", "zScales"),
  autoCor = TRUE,
  lag = 1,
  property = AAdata$Hydrophobicity$KyteDoolittle,
  property1 = AAdata$Hydrophobicity$KyteDoolittle,
  property2 = AAdata$Hydrophobicity$Eisenberg,
  center = TRUE,
  pH = 7,
  pKscale = "Lehninger",
  scale = "KyteDoolittle",
  monoisotopic = FALSE,
  avgScale = "expasy",
  aaShift = NULL,
  charge = 2,
  pKscale.PI = "EMBOSS"
)

Arguments

`peptides`	A vector of peptides with same length
`autoCor`	A logic value TRUE or FALSE, meaning to calculate autoCovariance value or not.
`lag`	A value for a lag, the max value is equal to the length of shortest peptide minus one. detail ref 'Peptides' package.
`property`	A property to use as value to be correlated.
`property1`	A property to use as value to evaluate the cross-covariance.
`property2`	A property to use as value to evaluate the cross-covariance.
`center`	A logic value TRUE or FALSE if the property must be centered
`pH`	A pH value in charge function.
`pKscale`	A character string specifying the pKa scale to be used; must be one of "Bjellqvist","Dawson", "EMBOSS", "Lehninger", "Murray", "Rodwell", "Sillero", "Solomon"or "Stryer"
`scale`	A character string specifying the hydophobicity scale to be used; must be one of "Aboderin", "AbrahamLeo", "Argos", "BlackMould", "BullBreese", "Casari","Chothia", "Cid", "Cowan3.4", "Cowan7.5", "Eisenberg", "Engelman", "Fasman","Fauchere", "Goldsack", "Guy", "HoppWoods", "Janin", "Jones", "Juretic","Kidera", "Kuhn", "KyteDoolittle", "Levitt", "Manavalan", "Miyazawa","Parker", "Ponnuswamy", "Prabhakaran", "Rao", "Rose", "Roseman", "Sweet","Tanford", "Welling", "Wilson", "Wolfenden", "Zimmerman", "interfaceScale_pH8","interfaceScale_pH2", "octanolScale_pH8", "octanolScale_pH2", "oiScale_pH8"or "oiScale_pH2".
`monoisotopic`	A logical value 'TRUE' or 'FALSE' indicating if monoisotopic weights of aminoacids should be used
`avgScale`	Set the mass scale to use for average weight only (if ’monoisotopic == FALSE’).Accepts "expasy" (default) or "mascot".
`aaShift`	Define the mass difference in Dalton of given amino acids as a named vector.Use the amino acid one letter code as names and the mass shift in Dalton as values.
`charge`	The net charge for which the m/z should be calculated
`pKscale.PI`	A character string specifying the pK scale in PI function to be used; must be one of "Bjellqvist","EMBOSS", "Murray", "Sillero", "Solomon", "Stryer", "Lehninger", "Dawson"or "Rodwell"

Value

a dataframe with all properties.

Examples

Neodataset.length <- Neodataset %>%
mutate(Length = str_length(wild_Peptide)) %>%
filter(Length == 9) %>%
unique()
peptides <- unique(Neodataset.length$wild_Peptide)
PropertyofPep(peptides)

yujijun/neoantigenML documentation built on March 20, 2022, 11:59 p.m.