xGR: Function to create a GRanges object given a list of genomic...

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

Description

xGR is supposed to create a GRanges object given a list of genomic regions.

Usage

xGR(
data,
format = c("chr:start-end", "data.frame", "bed", "GRanges"),
build.conversion = c(NA, "hg38.to.hg19", "hg18.to.hg19"),
add.name = TRUE,
remove.mcol = FALSE,
include.strand = FALSE,
verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

data	input genomic regions (GR). If formatted as "chr:start-end" (see the next parameter 'format' below), GR should be provided as a vector in the format of 'chrN:start-end', where N is either 1-22 or X, start (or end) is genomic positional number; for example, 'chr1:13-20'. If formatted as a 'data.frame', the first three columns correspond to the chromosome (1st column), the starting chromosome position (2nd column), and the ending chromosome position (3rd column). If the format is indicated as 'bed' (browser extensible data), the same as 'data.frame' format but the position is 0-based offset from chromomose position. If the genomic regions provided are not ranged but only the single position, the ending chromosome position (3rd column) is allowed not to be provided. The data could also be an object of 'GRanges' (in this case, formatted as 'GRanges')
format	the format of the input data. It can be one of "chr:start-end", "data.frame", "bed" or "GRanges"
build.conversion	the conversion from one genome build to another. The conversions supported are "hg38.to.hg19" and "hg18.to.hg19". By default it is NA (no need to do so)
add.name	logical to add names. By default, it sets to true
remove.mcol	logical to remove meta-columns. By default, it sets to false
include.strand	logical to include strand. By default, it sets to false. It only works when the format is "data.frame" or "bed" and the input data has 4 columns
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 GenomicRanges object

See Also

xLiftOver

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
# a) provide the genomic regions
## load ImmunoBase
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
RData.location=RData.location)
## get lead SNPs reported in AS GWAS and their significance info (p-values)
gr <- ImmunoBase$AS$variant
df <- as.data.frame(gr, row.names=NULL)
chr <- df$seqnames
start <- df$start
end <- df$end
data <- paste(chr,':',start,'-',end, sep='')

# b) create a GRanges object
GR <- xGR(data=data, format="chr:start-end",
RData.location=RData.location)

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.