Package 'PlinkMatrix'

Method: dim for delayed plink

Description

Method: dim for delayed plink

Usage

## S4 method for signature 'PlinkSeed'
dim(x)

Arguments

x	PlinkSeed instance

Value

2-vector

Examples

methods(class="PlinkSeed")

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Method: dimnames for delayed plink

Description

Method: dimnames for delayed plink

Usage

## S4 method for signature 'PlinkSeed'
dimnames(x)

Arguments

x	PlinkSeed instance

Value

list of dimnames

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sample GRanges coordinated with example_PlinkMatrix

Description

sample GRanges coordinated with example_PlinkMatrix

Usage

data("example_GRanges", package="PlinkMatrix")

Format

GRanges

Examples

data("example_GRanges", package="PlinkMatrix")
head(example_GRanges)

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produce PlinkMatrix from example data

Description

produce PlinkMatrix from example data

Usage

example_PlinkMatrix(folder = tempdir(), as_RSE = FALSE)

Arguments

folder	a path where unzipped example data will be managed
as_RSE	logical(1) if TRUE (default is FALSE) a RangedSummarizedExperiment is returned

Value

a SummarizedExperiment or RangedSummarizedExperiment with rowRanges calculated from SNP ids

Examples

example_PlinkMatrix()

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sample characteristics of 445 GEUVADIS samples

Description

sample characteristics of 445 GEUVADIS samples

Usage

data("g445samples", package="PlinkMatrix")

Format

data.frame

Note

Example data are those provided with tensorqtl, see https://github.com/broadinstitute/tensorqtl/tree/0c4db65a0cdc47f3b824ae530b89d270ef5e0096/example/data.

Examples

data("g445samples", package="PlinkMatrix")
g445samples[seq_len(4), seq_len(4)]

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operate with BiocFileCache to retrieve zip file of plink example data

Description

operate with BiocFileCache to retrieve zip file of plink example data

Usage

get_plink_example_path(ca = BiocFileCache::BiocFileCache())

Arguments

ca	BiocFileCache instance

Value

character string with path to example in cache

Examples

get_plink_example_path()

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Get sample metadata

Description

Get sample metadata

Usage

getSampleData(x)

Arguments

x	DelayedArray instance

Value

data.frame

Examples

tst <- example_PlinkMatrix()
head(getSampleData(tst))

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Get variant metadata

Description

Get variant metadata

Usage

getVariantData(x)

Arguments

x	DelayedArray instance

Value

data.frame

Examples

tst <- example_PlinkMatrix()
dim(getVariantData(tst))

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produce GRanges from variant notation for plink example from geuvadis

Description

produce GRanges from variant notation for plink example from geuvadis

Usage

plid2gr(x, sepused = "_")

Arguments

x	character vector of variant names
sepused	single character, defaults to "_"

Value

GRanges instance

Examples

plid2gr("chr18_80259028_AG_A_b38")

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Constructor for DelayedArray

Description

Constructor for DelayedArray

Usage

PlinkMatrix(filepath)

Arguments

filepath

path to plink bed, bim, fam resources without suffixes

Value

An instance of PlinkMatrix

Examples

PlinkMatrix

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Delayed interface to Plink genotype files

Description

This package includes C++ code to interface to Plink files. Large-scale genotype calls can be managed in a RangedSummarized Experiment instance.

Value

side effects

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read subset for use in delayed matrix approach

Description

read subset for use in delayed matrix approach

Usage

read_bed_subset(prefix, snp_indices, sample_indices, n_total_samples = NULL)

Arguments

prefix	character path to bed resources and file prefix
snp_indices	integer vector of snp indices
sample_indices	integer vector of sample indices
n_total_samples	optional

Value

matrix

Examples

read_bed_subset

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present seed concisely

Description

present seed concisely

Usage

## S4 method for signature 'PlinkSeed'
show(object)

Arguments

object

instance of PlinkSeed

Value

side effect of cat

Examples

ex <- example_PlinkMatrix()
ex

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