xPierEvidence: Function to extract evidence from a list of pNode objects

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xPierEvidence is supposed to extract evidence from a list of pNode objects, in terms of seed genes under genetic influence.

Usage

xPierEvidence(list_pNode, target.query = NULL, verbose = TRUE)

Arguments

list_pNode	a list of "pNode" objects or a "pNode" object
target.query	which gene is in query. If NULL, all genes will be queried
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

a data frame of nPair X 5 containing Gene-SNP pair info per context, where the 6 columns are "Gene" (seed genes), "SNP" (dbSNP), "Score" (an SNP's genetic influential score on a seed gene), "Context" (predictors), "Flag" (indicative of Lead SNPs or LD SNPs), and "Pval" (the SNP p-value)

Note

none

See Also

xPierEvidence

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
df_Gene2SNP <- xPierEvidence(ls_pNode)

## End(Not run)

Pi documentation built on Nov. 29, 2021, 3 p.m.