locus {locuszoomr}

Create locus object for plotting

Description

Creates object of class 'locus' for genomic locus plot similar to locuszoom.

Usage

locus(
  gene = NULL,
  data = NULL,
  xrange = NULL,
  seqname = NULL,
  flank = NULL,
  fix_window = NULL,
  ens_db,
  chrom = NULL,
  pos = NULL,
  p = NULL,
  yvar = NULL,
  labs = NULL,
  index_snp = NULL,
  LD = NULL
)

Arguments

gene

Optional character value specifying which gene to view. Either gene, or xrange plus seqname, or index_snp must be specified.

data

Dataset (data.frame or data.table) to use for plot. If unspecified or NULL, gene track information alone is returned.

xrange

Optional vector of genomic position range for the x axis.

seqname

Optional, specifies which chromosome to plot.

flank

Single value or vector with 2 values for how much flanking region left and right of the gene to show. Defaults to 100kb.

fix_window

Optional alternative to flank, which allows users to specify a fixed genomic window centred on the specified gene. Both flank and fix_window cannot be specified simultaneously.

ens_db

Either a character string which specifies which Ensembl database package (version 86 and earlier for Homo sapiens) to query for gene and exon positions (see ensembldb Bioconductor package). Or an ensembldb object which can be obtained from the AnnotationHub database. See the vignette and the AnnotationHub Bioconductor package for how to create this object.

chrom

Determines which column in data contains chromosome information. If NULL tries to autodetect the column.

pos

Determines which column in data contains position information. If NULL tries to autodetect the column.

p

Determines which column in data contains SNP p-values. If NULL tries to autodetect the column.

yvar

Specifies column in data for plotting on the y axis as an alternative to specifying p-values. Both p and yvar cannot be specified simultaneously.

labs

Determines which column in data contains SNP rs IDs. If NULL tries to autodetect the column.

index_snp

Specifies the index SNP. If not specified, the SNP with the lowest P value is selected. Can be used to specify locus region instead of specifying gene, or seqname and xrange.

LD

Optional character value to specify which column in data contains LD information.

Details

This is an R version of locuszoom (http://locuszoom.org) for generating publication ready Manhattan plots of gene loci. It references Ensembl databases using the ensembldb Bioconductor package framework for annotating genes and exons in the locus.

Value

Returns an object of class 'locus' ready for plotting, containing:

seqname

chromosome value

xrange

vector of genomic position range

gene

gene name

ens_db

Ensembl or AnnotationHub database version

chrom

column name in data containing chromosome information

pos

column name in data containing position

p

column name in data containing p-value

yvar

column name in data to be plotted on y axis as alternative to p

labs

column name in data containing SNP IDs

index_snp

id of the most significant SNP

data

the subset of GWAS data to be plotted

TX

dataframe of transcript annotations

EX

GRanges object of exon annotations

If data is NULL when locus() is called then gene track information alone is returned.

See Also

locus_plot() locus_ggplot() locus_plotly()

Examples

## Bioconductor package EnsDb.Hsapiens.v75 is needed for these examples
if(require(EnsDb.Hsapiens.v75)) {
data(SLE_gwas_sub)
loc <- locus(SLE_gwas_sub, gene = 'UBE2L3', flank = 1e5,
             ens_db = "EnsDb.Hsapiens.v75")
summary(loc)
locus_plot(loc)
loc2 <- locus(SLE_gwas_sub, gene = 'STAT4', flank = 1e5,
              ens_db = "EnsDb.Hsapiens.v75")
locus_plot(loc2)
}