calcIFIs: function to calculate the IFI (interference free index) of a...

In BenBruyneel/proteinDiscover: ProteinDiscover

function to calculate the IFI (interference free index) of a protein entry in the protein table of a pdResult files. Note this can only be calculated on the knockout proteins in the TKO control sample: see tmt10Channels or tmt11Channels for the eligible proteins

Description

function to calculate the IFI (interference free index) of a protein entry in the protein table of a pdResult files. Note this can only be calculated on the knockout proteins in the TKO control sample: see tmt10Channels or tmt11Channels for the eligible proteins

Usage

calcIFIs(
  db,
  selected = "His4",
  accession = knockOutProteins()$Accession[knockOutProteins()$short == selected],
  columns = "Abundances",
  groups = tmt11Channels(),
  IFIName = "IFI",
  calcFunc = mean,
  calcName = "mean",
  na.rm = TRUE
)

Arguments

db	database access 'handle'
selected	(short) name of the selected protein
accession	uniprot accession code of the selected protein. If parameter "selected" is one of the short names in knockOutProteins then doesn't need to be specified. Note that the accession does not need to be one of the accessions of the knockout proteins
columns	usually this will be "Abundances". It allows the selection of the correct (raw) columns as they come out of dfTransformRaws(), eg Abunances_1, Abundances_2, etc
groups	usually either tmt10Channels() or tmt11Channels: data.frame that specifies which (abundance) column belongs to which knock out group. Note that the 'selected' argument should be in groups
IFIName	specifies the name to give to the calculated values, usually "IFI"
calcFunc	function to be applied row-wise across the data.frame. Used in the calculation of the IFI values. Default = mean
calcName	name of the column with the calculated values in it, used in the related function calcData()
na.rm	default = TRUE. This specifies that NA's should be removed when using eg mean, median, etc

Value

a data.frame with two columns: one with the (short) name of the (selected) protein and one with the calculated values (named IFI)

BenBruyneel/proteinDiscover documentation built on March 16, 2024, 4:36 p.m.