Package 'haploR'

Converts vector of strings to numeric vector

Description

Converts vector of strings to numeric vector

Usage

as.num(x, na.strings = "NA")

Arguments

x	Input vector of strings.
na.strings	A string which represents NA. Default: "NA"

Value

A numeric vector

Examples

library(haploR)
as.num(c("1", "2", "X"), na.strings="X")

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This function queries HaploReg web-based tool in order to Extended view for SNP of interest

Description

This function queries HaploReg web-based tool in order to Extended view for SNP of interest

Usage

getExtendedView(snp, url = Haploreg.settings[["extended.view.url"]])

Arguments

snp	A SNP of interest.
url	A url to HaploReg. Default: <https://pubs.broadinstitute.org/mammals/haploreg/detail_v4.1.php?query=&id=>

Value

A list of tables t1, t2, ..., etc depending on information contained in HaploReg database.

Examples

tables <- getExtendedView(snp="rs10048158")
tables

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This function queries HaploReg web-based tool in order to see a list of GWAS.

Description

This function queries HaploReg web-based tool in order to see a list of GWAS.

Usage

getStudyList(url = Haploreg.settings[["study.url"]])

Arguments

url	A url to HaploReg. Default: <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>

Value

A list of studies. Each study is itself a list of two: name, id.

Examples

studies <- getStudyList()
studies

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This function queries HaploReg web-based tool and returns results.

Description

This function queries HaploReg web-based tool and returns results.

Usage

queryHaploreg(
  query = NULL,
  file = NULL,
  study = NULL,
  ldThresh = 0.8,
  ldPop = "EUR",
  epi = "vanilla",
  cons = "siphy",
  genetypes = "gencode",
  url = Haploreg.settings[["base.url"]],
  timeout = 100,
  encoding = "UTF-8",
  querySNP = FALSE,
  fields = NULL,
  verbose = FALSE
)

Arguments

query	Query (a vector of rsIDs).
file	A text file (one refSNP ID per line).
study	A particular study. See function getHaploRegStudyList(...). Default: NULL.
ldThresh	LD threshold, r2 (select NA to only show query variants). Default: 0.8.
ldPop	1000G Phase 1 population for LD calculation. Can be: "AFR", "AMR", "ASN". Default: "EUR".
epi	Source for epigenomes. Possible values: vanilla for ChromHMM (Core 15-state model); imputed for ChromHMM (25-state model using 12 imputed marks); methyl for H3K4me1/H3K4me3 peaks; acetyl for H3K27ac/H3K9ac peaks. Default: vanilla.
cons	Mammalian conservation algorithm. Possible values: gerp for GERP, siphy for SiPhy-omega, both for both. Default: siphy.
genetypes	Show position relative to. Possible values: gencode for Gencode genes; refseq for RefSeq genes; both for both. Default: gencode.
url	HaploReg url address. Default: <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>
timeout	A timeout parameter for curl. Default: 100
encoding	sets the encoding for correct retrieval web-page content. Default: UTF-8
querySNP	A flag indicating to return query SNPs only. Default: FALSE
fields	A set of fields to extract. Refer to the package vignette for available fields. Default: All.
verbose	Verbosing output. Default: FALSE.

Value

A data frame (table) with results similar to HaploReg uses.

Examples

library(haploR)
data <- queryHaploreg(c("rs10048158","rs4791078"))
head(data)

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This function queries RegulomeDB web-based tool and returns results in a data frame.

Description

This function queries RegulomeDB web-based tool and returns results in a data frame.

Usage

queryRegulome(
  query = NULL,
  genomeAssembly = "GRCh37",
  limit = 1000,
  timeout = 100
)

Arguments

query	Query (a vector of rsIDs or exact one query region in rsid or like "chr1:39492461-39492462").
genomeAssembly	Genome assembly built: can be GRCh37 (default) or GRCh38.
limit	It controls how many variants will be queried and returned for a large region. It can be a number (1000 by default) or "all". Please note that large number or "all" may get yourself hurt because you could get timeout or may even crash the server.
timeout	A timeout parameter for httr::GET. Default: 100

Value

a data frame (table) OR a list with the following items: - guery_coordinates - features - regulome_score - variants - nearby_snps, - assembly

Examples

data <- queryRegulome(c("rs4791078","rs10048158"))
head(data)

---

This function queries RegulomeDB web-based tool and returns results in a data frame.

Description

This function queries RegulomeDB web-based tool and returns results in a data frame.

This function queries RegulomeDB web-based tool and returns results in a data frame.

Usage

regulomeSearch(
  query = NULL,
  genomeAssembly = NULL,
  limit = 1000,
  timeout = 100
)

regulomeSummary(
  query = NULL,
  limit = 1000,
  genomeAssembly = NULL,
  timeout = 100
)

Arguments

query	Query (a vector of rsIDs).
genomeAssembly	Genome assembly built: can be GRCh37 or GRCh38
limit	It controls how many variants will be queried and returned for a large region. It can be a number (1000 by default) or "all". Please note that large number or "all" may get yourself hurt because you could get timeout or may even crash the server.
timeout	A timeout parameter for httr::GET. Default: 100

Value

a list with the following items: - guery_coordinates - features - regulome_score - variants - nearby_snps, - assembly

a data frame (table)

Examples

data <- regulomeSearch("rs4791078")
head(data)
data <- regulomeSummary(c("rs4791078","rs10048158"))
head(data)

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