xPierTrackR Documentation

Function to visualise prioritised genes using track plot

Description

xPierTrack is supposed to visualise prioritised genes using track plot. Priority for the gene in query is displayed on the data track and nearby genes on the annotation track. Genomic locations on the X-axis are indicated on the X-axis, and the gene in query is highlighted.

Usage

xPierTrack(pNode, priority.top = NULL, target.query = NULL,
window = 1e+06, nearby = NULL, query.highlight = TRUE,
GR.Gene = c("UCSC_knownGene", "UCSC_knownCanonical"), verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

pNode

an object of class "pNode" (or "pTarget" or "dTarget")

priority.top

the number of the top targets used for track plot. By default, it is NULL meaning all targets are used

target.query

which gene in query will be visualised. If NULL, the target gene with the top priority will be displayed

window

the maximum distance defining nearby genes around the target gene in query. By default it is 1e6

nearby

the maximum number defining nearby genes around the target gene in query. By default it is NULL. If not NULL, it will overwrite the parameter 'window'

query.highlight

logical to indicate whether the gene in query will be highlighted

GR.Gene

the genomic regions of genes. By default, it is 'UCSC_knownGene', that is, UCSC known genes (together with genomic locations) based on human genome assembly hg19. It can be 'UCSC_knownCanonical', that is, UCSC known canonical genes (together with genomic locations) based on human genome assembly hg19. Alternatively, the user can specify the customised input. To do so, first save your RData file (containing an GR object) into your local computer, and make sure the GR object content names refer to Gene Symbols. Then, tell "GR.Gene" with your RData file name (with or without extension), plus specify your file RData path in "RData.location"

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display

RData.location

the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

an object of class "ggplot", appended by an GR object called 'gr'

Note

none

See Also

xMLrandomforest

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) perform priority analysis
pNode <- xPierSNPs(data=AS, include.eQTL="JKng_mono",
include.HiC='Monocytes', network="PCommonsUN_medium", restart=0.7,
RData.location=RData.location)

# c) track plot
library(Gviz)
#pdf(file="Gene_tracks.pdf", height=4, width=10, compress=TRUE)
xPierTrack(pNode, RData.location=RData.location)
#dev.off()
xPierTrack(pNode, priority.top=1000, nearby=20,
RData.location=RData.location)

## End(Not run)