calcAllIFIs: Wrapper function that uses 'tmt11Channels' to calculate the...

In BenBruyneel/proteinDiscover: ProteinDiscover

Wrapper function that uses tmt11Channels to calculate the IFI's for a set of (knock out) protein channels

Description

Wrapper function that uses tmt11Channels to calculate the IFI's for a set of (knock out) protein channels

Usage

calcAllIFIs(
  db,
  proteinsKnockedOut = knockOutProteins()$short[knockOutProteins()$knockout],
  accession = NA,
  groups = tmt11Channels(),
  joined = TRUE
)

Arguments

db	database access 'handle'
proteinsKnockedOut	character vector that specifies the (knock out) protein channels for which the IFI's are to be calculated
accession	single element character vector specifying the accession of the protein whose abundances are to be used for the IFI calculation
groups	usually either tmt10Channels() or tmt11Channels: data.frame that specifies which (abundance) column belongs to which knock out group
joined	defines the type of output: if TRUE then a single data.frame with all IFI's for all (knock out) proteins is generated. Otherwise a list of data.frame's is generated for all proteins separately

Value

a data.frame with two columns: one with the (short) name of the (selected) proteins and one with the calculated values (named IFI) or a list of data.frame's with the same structure

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