xGRsort: Function to sort by chromosomes/seqnames, start and end...
In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description
Usage
Arguments
Value
See Also
Examples
Description
xGRsort is supposed to sort by chromosomes/seqnames, start and
end coordinates of the intervals.
Usage
1
Arguments
data
input genomic regions (GR). 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'
Value
index
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
## 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"
# 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
cse <- xGRcse(gr)
# b) sort index
ind <- xGRsort(cse)
data <- cse[ind]
## End(Not run)
XGR documentation built on June 18, 2019, 3:01 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value See Also Examples
Description
xGRsort is supposed to sort by chromosomes/seqnames, start and
end coordinates of the intervals.
Usage
1 |
Arguments
data |
input genomic regions (GR). 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' |
Value
index
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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"
# 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
cse <- xGRcse(gr)
# b) sort index
ind <- xGRsort(cse)
data <- cse[ind]
## End(Not run)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.