readPWdata: Read in pathway database data needed for pathway...

In pwOmics: Pathway-based data integration of omics data

Description

This function reads pathway data of the chosen database(s) via the AnnotationHub [1] package and rBiopaxParser [2] package. Takes a lot of time for a high number of proteins and/or if all databases are chosen. First, chosen databases are retrieved, then new internal pathway IDs are generated. Afterwards the genelists of the different databases are loaded or generated, depending on the loadgenelists option. Pathway ID mapping takes some time, especially for such big databases as reactome, so the genelists are automatically stored in the current working folder and can be used via loadgenelists in case you use this function again for easier and faster usage... Biopax level of retrieved databases is 2 by default.

Usage

readPWdata(data_omics, loadgenelists, biopax_level = 2)

Arguments

data_omics	OmicsData object.
loadgenelists	path of genelist RData files stored previously; all genelists stored in this path are read in and used automatically if path is given; if loadgenelists = FALSE, then genelists from pathway databases have to be generated first.
biopax_level	integer indicating biopax level of pathway database information. default level is 2.

Value

list of OmicsData object and genelists for selected pathway databases.

References

1. Morgan M, Carlson M, Tenenbaum D and Arora S. AnnotationHub: Client to access AnnotationHub resources. R package version 1.99.75.

2. Kramer F, Bayerlova M, Klemm F, Bleckmann A and Beissbarth T. rBiopaxParser - an R package to parse, modify and visualize BioPAX data.

Examples

## Not run: 
data(OmicsExampleData)
data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24), 
tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
PWdatabase = c("biocarta", "kegg", "nci", "reactome"), 
TFtargetdatabase = c("userspec"))
data_omics = readPhosphodata(data_omics, 
phosphoreg = system.file("extdata", "phospho_reg_table.txt", 
package = "pwOmics.newupdown")) 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics.newupdown"))
data_omics_plus = readPWdata(data_omics,  
loadgenelists = system.file("extdata/Genelists", package = "pwOmics.newupdown"))

## End(Not run)

pwOmics documentation built on Nov. 8, 2020, 4:55 p.m.