Package 'gwasvcf'

Title: Tools for Dealing with GWAS Summary Data in VCF Format
Description: Tools for dealing with GWAS summary data in VCF format. Includes reading, querying, writing, as well as helper functions such as LD proxy searches.
Authors: Gibran Hemani [aut, cre] , Tom Palmer [ctb] , Rita Rasteiro [ctb]
Maintainer: Gibran Hemani <[email protected]>
License: MIT + file LICENSE
Version: 0.1.2
Built: 2024-09-24 03:45:54 UTC
Source: https://github.com/MRCIEU/gwasvcf

Help Index

Check if the tools_bcftools option is set

Description

See set_bcftools() for more information

Usage

check_bcftools()

Value

TRUE or FALSE

Check if the tools_plink option is set

Description

See set_plink() for more information

Usage

check_plink()

Value

TRUE or FALSE

Create LD reference sqlite database for tags

Description

This is used for looking up proxies

Usage

create_ldref_sqlite(bfile, dbname, tag_r2 = 0.6)

Arguments

bfile

path to plink file
dbname

dbname to produce (overwrites existing if exists)
tag_r2

minimum tag r2

Create pval index from GWAS-VCF file

Description

Create a separate file called ⁠<id>.pvali⁠ which is used to speed up p-value queries.

Usage

create_pval_index_from_vcf(vcffile, maximum_pval, indexname)

Arguments

vcffile

VCF filename
maximum_pval

Maximum p-value to include. Default = 0.05
indexname

index file name to create. Deletes existing file if exists.

Create RSID index from VCF

Description

Create RSID index from VCF

Usage

create_rsidx_index_from_vcf(vcf, indexname)

Arguments

vcf

VCF filename
indexname

index file name to create. Deletes existing file if exists.

Create new index from existing index using a subset of rsids

Description

Note this requires a modified version of plink that allows ld-window-r2 flag for –r option. Available here: https://github.com/explodecomputer/plink-ng

Usage

create_rsidx_sub_index(rsid, rsidx, newindex)

Arguments

rsid

Vector of rsids
rsidx

Existing index
newindex

New index (Note: will delete existing file if exists)

Value

NULL, creates new index file

Create GWAS vcf

Description

Create GWAS vcf

Usage

create_vcf(
  chrom,
  pos,
  nea,
  ea,
  snp = NULL,
  ea_af = NULL,
  effect = NULL,
  se = NULL,
  pval = NULL,
  n = NULL,
  ncase = NULL,
  name = NULL
)

Arguments

chrom

chrom vector
pos

pos vector
nea

nea vector
ea

ea vector
snp

Optional vector
ea_af

Optional vector
effect

Optional vector
se

Optional vector
pval

Optional vector
n

Optional vector
ncase

Optional vector
name

Optional vector

Value

vcf object

Find LD proxies for a set of SNPs

Description

Find LD proxies for a set of SNPs

Usage

get_ld_proxies(
  rsid,
  bfile,
  searchspace = NULL,
  tag_kb = 5000,
  tag_nsnp = 5000,
  tag_r2 = 0.6,
  threads = 1,
  out = tempfile()
)

Arguments

rsid

list of rs IDs
bfile

ld reference panel
searchspace

Optional list of rs IDs to use as potential proxies
tag_kb

=5000 Proxy parameter
tag_nsnp

=5000 Proxy parameter
tag_r2

=0.6 Proxy parameter
threads

Number of threads to use (=1)
out

temporary output file

Value

data frame

Create a SummarySet

Description

Returns a gwasglue2 SummarySet object

Usage

gwasvcf_to_summaryset(vcf)

Arguments

vcf

Path or URL to GWAS-VCF file or VCF object e.g. output from VariantAnnotation::readVcf(), create_vcf() or query_gwas()

Merge two GWAS VCF objects

Description

Returns merged intersection of two VCF objects

Usage

merge_vcf(a, b)

Arguments

a

VCF object
b

VCF object

Value

SimpleList of VCF objects

Parse chromosome:position

Description

Takes data frame or vector of chromosome position ranges and parses to granges object

Usage

parse_chrompos(chrompos, radius = NULL)

Arguments

chrompos

Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns chrom, start, end.
radius

Add radius to the specified positions. Default = NULL

Value

GRanges object

Extract SNPs from vcf file

Description

Finds proxies if necessary

Usage

proxy_match(
  vcf,
  rsid,
  bfile = NULL,
  proxies = "yes",
  tag_kb = 5000,
  tag_nsnp = 5000,
  tag_r2 = 0.6,
  threads = 1,
  rsidx = NULL,
  dbfile = NULL
)

Arguments

vcf

vcf file name
rsid

list of rs IDs
bfile

ld reference panel (plink)
proxies

="yes" If SNPs are absent then look for proxies (yes) or not (no). Can also mask all target SNPs and only return proxies (only), for testing purposes
tag_kb

=5000 Proxy parameter
tag_nsnp

=5000 Proxy parameter
tag_r2

=0.6 Proxy parameter
threads

Number of threads to use (=1)
rsidx

Path to rsidx index
dbfile

ld tag database (sqlite)

Value

data frame

Query chromosome and position using bcftools

Description

Query chromosome and position using bcftools

Usage

query_chrompos_bcftools(chrompos, vcffile, id = NULL)

Arguments

chrompos

Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns chrom, start, end.
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter

Value

vcf object

Query vcf file, extracting by chromosome and position

Description

Query vcf file, extracting by chromosome and position

Usage

query_chrompos_file(chrompos, vcffile, id = NULL, build = "GRCh37")

Arguments

chrompos

Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns chrom, start, end.
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter
build

Default="GRCh37" Build of vcffile

Value

VCF object

Query chrompos from vcf object

Description

Query chrompos from vcf object

Usage

query_chrompos_vcf(chrompos, vcf, id = NULL)

Arguments

chrompos

Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns chrom, start, end.
vcf

VCF object (e.g. from readVcf)
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter

Value

VCF object

Query data from vcf file

Description

Read in GWAS summary data with filters on datasets (if multiple datasets per file) and/or chromosome/position, rsids or pvalues. Chooses most optimal choice for the detected operating system. Typically chrompos searches are the fastest. On Windows, rsid or pvalue filters from a file will be slow.

Usage

query_gwas(
  vcf,
  chrompos = NULL,
  rsid = NULL,
  pval = NULL,
  id = NULL,
  rsidx = NULL,
  pvali = NULL,
  build = "GRCh37",
  os = Sys.info()[["sysname"]],
  proxies = "no",
  bfile = NULL,
  dbfile = NULL,
  tag_kb = 5000,
  tag_nsnp = 5000,
  tag_r2 = 0.6,
  threads = 1
)

Arguments

vcf

Path or URL to GWAS-VCF file or VCF object e.g. output from VariantAnnotation::readVcf() or create_vcf()
chrompos

Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns chrom, start, end.
rsid

Vector of rsids
pval

P-value threshold (NOT -log10)
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter
rsidx

Path to rsidx index file
pvali

Path to pval index file
build

="GRCh37" Build of vcffile
os

The operating system. Default is as detected. Determines the method used to perform query
proxies

="no" If SNPs are absent then look for proxies (yes) or not (no). Can also mask all target SNPs and only return proxies (only), for testing purposes. Currently only possible if querying rsid.
bfile

=path to plink bed/bim/fam ld reference panel
dbfile

=path to sqlite tag snp database
tag_kb

=5000 Proxy parameter
tag_nsnp

=5000 Proxy parameter
tag_r2

=0.6 Proxy parameter
threads

=1 NUmber of threads

Value

vcf object

Query p-value using bcftools

Description

Query p-value using bcftools

Usage

query_pval_bcftools(pval, vcffile, id = NULL)

Arguments

pval

P-value threshold (NOT -log10)
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter

Value

vcf object

Query pval from vcf file

Description

Query pval from vcf file

Usage

query_pval_file(pval, vcffile, id = NULL, build = "GRCh37")

Arguments

pval

P-value threshold (NOT -log10)
vcffile

Path to tabix indexed vcf file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter
build

Default="GRCh37"

Value

VCF object

Query pval from file using pvali index

Description

See create_pvali_index

See create_pvali_index

Usage

query_pval_sqlite3(pval, vcffile, id = NULL, pvali)

query_pval_sqlite3(pval, vcffile, id = NULL, pvali)

Arguments

pval

pval threshold
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter
pvali

Path to pval index file

Value

vcf object

vcf object

Query based on p-value threshold from vcf

Description

Query based on p-value threshold from vcf

Usage

query_pval_vcf(pval, vcf, id = NULL)

Arguments

pval

P-value threshold (NOT -log10)
vcf

VCF object (e.g. from readVcf)
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter

Value

VCF object

Query pvali

Description

Query pvali

Query pvali

Usage

query_pvali(pval, pvali)

query_pvali(pval, pvali)

Arguments

pval

pval threshold
pvali

Path to pval index file

Value

data frame

data frame

Query

Description

Query

Usage

query_rsid_bcftools(rsid, vcffile, id = NULL)

Arguments

rsid

Vector of rsids
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter

Value

VCF object

Query vcf file, extracting by rsid

Description

Query vcf file, extracting by rsid

Usage

query_rsid_file(rsid, vcffile, id = NULL, build = "GRCh37")

Arguments

rsid

Vector of rsids. Use DBSNP build (???)
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter
build

Default="GRCh37" Build of vcffile

Value

VCF object

Query rsid from file using rsidx index

Description

See create_rsidx_index

Usage

query_rsid_rsidx(rsid, vcffile, id = NULL, rsidx)

Arguments

rsid

Vector of rsids
vcffile

Path to .vcf.gz GWAS summary data file
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter
rsidx

Path to rsidx index file

Value

vcf object

Query rsid from vcf object

Description

Query rsid from vcf object

Usage

query_rsid_vcf(rsid, vcf, id = NULL)

Arguments

rsid

Vector of rsids
vcf

VCF object (e.g. from readVcf)
id

If multiple GWAS datasets in the vcf file, the name (sample ID) from which to perform the filter

Value

VCF object

Query rsidx

Description

Query rsidx

Usage

query_rsidx(rsid, rsidx)

Arguments

rsid

Vector of rsids
rsidx

Path to rsidx index file

Value

data frame

Set bcftools binary location

Description

Set bcftools binary location

Usage

set_bcftools(path = "")

Arguments

path

If "" (default), then will use the MRCIEU/genetics.binaRies to get binaries that are appropriate for the detected operating system. Otherwise, provide the path to the bcftools binary. If NULL then will set the option to NULL.

Value

NULL, sets option 'tools_bcftools'

Set plink binary location

Description

Set plink binary location

Usage

set_plink(path = "")

Arguments

path

If "" (default), then will use the MRCIEU/genetics.binaRies to get binaries that are appropriate for the detected operating system. Otherwise, provide the path to the plink binary. If NULL then will set the option to NULL.

Value

NULL, sets option 'tools_plink'

Lookup LD proxies from sqlite database

Description

Lookup LD proxies from sqlite database

Usage

sqlite_ld_proxies(rsids, dbfile, tag_r2)

Arguments

rsids

List of rsids
dbfile

path to dbfile
tag_r2

minimum r2 value

Value

data frame

VariantAnnotation

Description

VariantAnnotation

Convert vcf format to granges format

Description

Convert vcf format to granges format

Usage

vcf_to_granges(vcf, id = NULL)

Arguments

vcf

Output from readVcf
id

Only accepts one ID, so specify here if there are multiple GWAS datasets in the vcf

Value

GRanges object

Convert vcf format to tibble (data frame)

Description

Convert vcf format to tibble (data frame)

Usage

vcf_to_tibble(vcf, id = NULL)

Arguments

vcf

Output from readVcf
id

Only accepts one ID, so specify here if there are multiple GWAS datasets in the vcf

Value

GRanges object

Reduce list of VCFs to intersecting regions

Description

Reduce list of VCFs to intersecting regions

Usage

vcflist_overlaps(vcflist, chrompos)

Arguments

vcflist

List of VCF objects, or list of VCF filenames, or mix of VCF objects and filenames
chrompos

Either vector of chromosome and position ranges e.g. "1:1000" or "1:1000-2000", or data frame with columns chrom, start, end.

Value

List of VCFs