getAliasfromSTRINGIDs: Map alias names to STRING IDs of consensus graph.

In MarenS2/pwOmics_maren: Pathway-based data integration of omics data

Description

Map alias names to STRING IDs of consensus graph.

Usage

getAliasfromSTRINGIDs(data_omics, ST_net, updown = FALSE, phospho = TRUE,
  consSTRINGIDs, tps, string_db)

Arguments

data_omics	OmicsData object.
ST_net	steiner tree graph generated by SteinerTree_cons function.
updown	boolean value; TRUE in case up- and downregulation should be checked individually for intersection. Type of checking is defined with parameter 'phospho'.
phospho	boolean value; TRUE in case up- and downregulation should be checked based on provided downstream phosphoprotein influence from identifyPR function; FALSE in case up- and downregulation should be checked for without phosphoprotein database knowledge. Default is TRUE.
consSTRINGIDs	first element of list generated by getConsensusSTRINGIDs function; a data.frame including the proteins to be considered as terminal nodes in Steiner tree with colnames ST_proteins and the corresponding STRING IDs in column 'STRING_id'.
tps	integer specifying current timepoint under consideration.
string_db	second element of list generated by getConsensusSTRINGIDs function; species table (for human) of STRING database.

Value

igraph object with alias name annotation.

MarenS2/pwOmics_maren documentation built on May 6, 2019, 3:27 p.m.