convertSifnxIds {paxtoolsr}R Documentation

Convert IDs in a SIFNX

Description

Convert IDs in a SIFNX

Usage

convertSifnxIds(sifnx, participantType = "ProteinReference",
  idType = "NCBI Gene", mapping = NULL, naRm = TRUE)

Arguments

sifnx

a SIFNX object (e.g. from the downloadPc2 function)

participantType

the type of participant on which the conversion will occur. Important because not all ID types apply to all entities and otherwise those entities would be labeled as missing an ID.

idType

an ID type for conversion (not used if mapping parameter used)

mapping

a two column data.frame with columns mapping$PARTICIPANT (old IDs to convert from) and mapping$ID (new IDs to convert to)

naRm

remove edges where NA's were introduced due to failed conversions

Value

a SIFNX list with nodes and edges. Only edges will have converted IDs


[Package paxtoolsr version 1.14.0 Index]