xLiftOver: Function to lift genomic intervals from one genome build to...

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

Description

xLiftOver is supposed to lift genomic intervals from one genome build to another. Supported are the conversions between genome builds 'hg38' (GRCh38), 'hg19' (GRCh37) and 'h18'.

Usage

xLiftOver(
data.file,
format.file = c("data.frame", "bed", "chr:start-end", "GRanges"),
build.conversion = c(NA, "hg38.to.hg19", "hg19.to.hg38",
"hg19.to.hg18",
"hg18.to.hg38", "hg18.to.hg19"),
merged = T,
verbose = T,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

data.file	an input data file, containing a list of genomic regions to test. If the input file is formatted as a 'data.frame' (specified by the parameter 'format.file' below), 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. If the format is indicated as "chr:start-end", instead of using the first 3 columns, only the first column will be used and processed. If the file also contains other columns, these additional columns will be ignored. Alternatively, the input file can be the content itself assuming that input file has been read. Note: the file should use the tab delimiter as the field separator between columns
format.file	the format for input files. It can be one of "data.frame", "chr:start-end", "bed"
build.conversion	the conversion from one genome build to another. The conversions supported are "hg38.to.hg19", "hg19.to.hg38", "hg19.to.hg18", "hg18.to.hg38" and "hg18.to.hg19". By default it is NA, forcing the user to specify the corrent one.
merged	logical to indicate whether multiple ranges should be merged into the one per a range in query. By default, it sets to true
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
guid	a valid (5-character) Global Unique IDentifier for an OSF project. See xRDataLoader for details

Value

an GR oject storing converted genomic intervals.

See Also

xLiftOver

Examples

## Not run: 
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

# Provide UCSC genes (hg19)
UCSC_genes <- xRDataLoader(RData.customised='UCSC_genes',
RData.location=RData.location)
UCSC_genes

# Lift over to hg38
gr <- xLiftOver(UCSC_genes, format.file="GRanges",
build.conversion="hg19.to.hg38", RData.location=RData.location)
gr

## End(Not run)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: dnet
Loading required package: supraHex
Loading required package: hexbin
Loading required package: ggplot2
Start at 2020-04-13 05:50:13

Attempt to download from https://github.com/hfang-bristol/RDataCentre/blob/master/Portal/UCSC_genes.RData?raw=true (at 2020-04-13 05:50:14)
Attempt to download from http://galahad.well.ox.ac.uk/bigdata/UCSC_genes.RData (at 2020-04-13 05:50:16)
Attempt to download from http://galahad.well.ox.ac.uk/bigdata/UCSC_genes.RData (at 2020-04-13 05:50:17)
'UCSC_genes' CANNOT be loaded (at 2020-04-13 05:50:18)

End at 2020-04-13 05:50:18
Runtime in total is: 5 secs

NULL
Start at 2020-04-13 05:50:18

First, import the files formatted as 'GRanges' (2020-04-13 05:50:18) ...
	import the data file (2020-04-13 05:50:18) ...
Warning messages:
1: In is.na(data.file) :
  is.na() applied to non-(list or vector) of type 'NULL'
2: In xLiftOver(UCSC_genes, format.file = "GRanges", build.conversion = "hg19.to.hg38",  :
  The file 'data.file' must be provided!

NULL

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