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

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

Function to lift genomic intervals from one genome build to another.

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 = TRUE,
verbose = TRUE,
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

xRDataLoader

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 

# Provide UCSC known genes (hg19)
UCSC_genes <- xRDataLoader('UCSC_knownGene',
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)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.