xSNP2eGenes: Function to define eQTL genes given a list of SNPs or a...

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

xSNP2eGenes is supposed to define eQTL genes given a list of SNPs or a customised eQTL mapping data. The eQTL weight is calcualted as Cumulative Distribution Function of negative log-transformed eQTL-reported signficance level.

Usage

xSNP2eGenes(
data,
include.eQTL = NA,
eQTL.customised = NULL,
cdf.function = c("empirical", "exponential"),
plot = FALSE,
verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

data	an input vector containing SNPs. SNPs should be provided as dbSNP ID (ie starting with rs). Alternatively, they can be in the format of 'chrN:xxx', where N is either 1-22 or X, xxx is number; for example, 'chr16:28525386'
include.eQTL	the eQTL supported currently. By default, it is 'NA' to disable this option. Pre-built eQTL datasets are detailed in xDefineEQTL
eQTL.customised	a user-input matrix or data frame with 4 columns: 1st column for SNPs/eQTLs, 2nd column for Genes, 3rd for eQTL mapping significance level (p-values or FDR), and 4th for contexts (required even though only one context is input). Alternatively, it can be a file containing these 4 columns. It is designed to allow the user analysing their eQTL data. This customisation (if provided) will populate built-in eQTL data
cdf.function	a character specifying a Cumulative Distribution Function (cdf). It can be one of 'exponential' based on exponential cdf, 'empirical' for empirical cdf
plot	logical to indicate whether the histogram plot (plus density or CDF plot) should be drawn. By default, it sets to false for no plotting
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
RData.location	the characters to tell the location of built-in RData files. See xRDataLoader for details
guid	a valid (5-character) Global Unique IDentifier for an OSF project. See xRDataLoader for details

Value

a data frame with following columns:

• Gene: eQTL-containing genes

• SNP: eQTLs

• Sig: the eQTL mapping significant level (the best/minimum)

• Weight: the eQTL weight

Note

none

See Also

xRDataLoader

Examples

## Not run: 
# Load the library
library(XGR)

## End(Not run)

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
# a) provide the SNPs with the significance info
data(ImmunoBase)
gr <- ImmunoBase$AS$variants
AS <- as.data.frame(GenomicRanges::mcols(gr)[, c('Variant','Pvalue')])

# b) define eQTL genes
df_eGenes <- xSNP2eGenes(data=AS[,1], include.eQTL="JKscience_TS2A",
RData.location=RData.location)

## End(Not run)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.