xSNPeqtlR Documentation

Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data

Description

xSNPeqtl is supposed to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data.

Usage

xSNPeqtl(data = NULL, include.eQTL = c(NA, "JKscience_TS2A",
"JKscience_TS2A_CD14", "JKscience_TS2A_LPS2", "JKscience_TS2A_LPS24",
"JKscience_TS2A_IFN", "JKscience_TS2B", "JKscience_TS2B_CD14",
"JKscience_TS2B_LPS2", "JKscience_TS2B_LPS24", "JKscience_TS2B_IFN",
"JKscience_TS3A", "JKng_bcell", "JKng_bcell_cis", "JKng_bcell_trans",
"JKng_mono", "JKng_mono_cis", "JKng_mono_trans", "JKnc_neutro",
"JKnc_neutro_cis", "JKnc_neutro_trans", "JK_nk",
"GTEx_V4_Adipose_Subcutaneous", "GTEx_V4_Artery_Aorta",
"GTEx_V4_Artery_Tibial", "GTEx_V4_Esophagus_Mucosa",
"GTEx_V4_Esophagus_Muscularis", "GTEx_V4_Heart_Left_Ventricle",
"GTEx_V4_Lung", "GTEx_V4_Muscle_Skeletal", "GTEx_V4_Nerve_Tibial",
"GTEx_V4_Skin_Sun_Exposed_Lower_leg", "GTEx_V4_Stomach",
"GTEx_V4_Thyroid",
"GTEx_V4_Whole_Blood", "eQTLdb_NK", "eQTLdb_CD14", "eQTLdb_LPS2",
"eQTLdb_LPS24", "eQTLdb_IFN"), eQTL.customised = NULL, verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

data

NULL or a input vector containing SNPs. If NULL, all SNPs will be considered. If a 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

genes modulated by eQTL (also Lead SNPs or in LD with Lead SNPs) are also included. By default, it is 'NA' to disable this option. Otherwise, those genes modulated by eQTL will be included. Pre-built eQTL datasets are detailed in the section 'Note'

eQTL.customised

a user-input matrix or data frame with 3 columns: 1st column for SNPs/eQTLs, 2nd column for Genes, and 3rd for eQTL mapping significance level (p-values or FDR). It is designed to allow the user analysing their eQTL data. This customisation (if provided) has the high priority over built-in eQTL data.

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

Value

a data frame with following columns:

Note

Pre-built eQTL datasets are described below according to the data sources.
1. Context-specific eQTLs in monocytes: resting and activating states. Sourced from Science 2014, 343(6175):1246949

2. eQTLs in B cells. Sourced from Nature Genetics 2012, 44(5):502-510

3. eQTLs in monocytes. Sourced from Nature Genetics 2012, 44(5):502-510

4. eQTLs in neutrophils. Sourced from Nature Communications 2015, 7(6):7545

5. eQTLs in NK cells. Unpublished

6. Tissue-specific eQTLs from GTEx (version 4; incuding 13 tissues). Sourced from Science 2015, 348(6235):648-60

See Also

xRDataLoader

Examples

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

## End(Not run)

RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev"
# a) provide the SNPs with the significance info
## get lead SNPs reported in AS GWAS and their significance info (p-values)
#data.file <- "http://galahad.well.ox.ac.uk/bigdata/AS.txt"
#AS <- read.delim(data.file, header=TRUE, stringsAsFactors=FALSE)
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
RData.location=RData.location)
gr <- ImmunoBase$AS$variants
AS <- as.data.frame(GenomicRanges::mcols(gr)[, c('Variant','Pvalue')])

## Not run: 
# b) define eQTL genes
df_SGS <- xSNPeqtl(data=AS[,1], include.eQTL="JKscience_TS2A",
RData.location=RData.location)

## End(Not run)