Package 'EthSEQ'

Title: Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data
Description: Reliable and rapid ethnicity annotation from whole exome and targeted sequencing data.
Authors: Alessandro Romanel [aut, cre], Davide Dalfovo [aut]
Maintainer: Alessandro Romanel <alessandro.romanel@unitn.it>
License: GPL-3
Version: 3.0.2
Built: 2024-02-18 07:59:01 UTC
Source: CRAN

Help Index


Ancestry analysis from whole-exome and targeted sequencing data

Description

This function performs ancestry analysis of a set of samples ad reports the results.

Usage

ethseq.Analysis(
  target.vcf = NA,
  target.gds = NA,
  bam.list = NA,
  out.dir = tempdir(),
  model.gds = NA,
  model.available = NA,
  model.assembly = "hg38",
  model.pop = "All",
  model.folder = tempdir(),
  run.genotype = FALSE,
  aseq.path = tempdir(),
  mbq = 20,
  mrq = 20,
  mdc = 10,
  cores = 1,
  verbose = TRUE,
  composite.model.call.rate = 1,
  refinement.analysis = NA,
  space = "2D",
  bam.chr.encoding = FALSE
)

Arguments

target.vcf

Path to the sample's genotypes in VCF format

target.gds

Path to the sample's genotypes in GDS format

bam.list

Path to a file containing a list of BAM files paths

out.dir

Path to the folder where the output of the analysis is saved

model.gds

Path to a GDS file specifying the reference model

model.available

String specifying the pre-computed reference model to use

model.assembly

String value indicating the assembly version to download for the pre-build models

model.pop

String value indicating the population to download for the pre-build models

model.folder

Path to the folder where reference models are already present or downloaded when needed

run.genotype

Logical values indicating whether the ASEQ genotype should be run

aseq.path

Path to the folder where ASEQ binary is available or is downloaded when needed

mbq

Minmum base quality used in the pileup by ASEQ

mrq

Minimum read quality used in the piluep by ASEQ

mdc

Minimum read count acceptable for genotype inference by ASEQ

cores

Number of parallel cores used for the analysis

verbose

Print detailed information

composite.model.call.rate

SNP call rate used to run Principal Component Analysis (PCA)

refinement.analysis

Matrix specifying a tree of ancestry sets

space

Dimensions of PCA space used to infer ancestry (2D or 3D)

bam.chr.encoding

Logical value indicating whether input BAM files have chromosomes encoded with "chr" prefix

Value

Logical value indicating the success of the analysis


Create Reference Model for Ancestry Analysis

Description

This function creates a GDS reference model that can be used to performe EthSEQ ancestry analysis

Usage

ethseq.RM(
  vcf.fn,
  annotations,
  out.dir = "./",
  model.name = "Reference.Model",
  bed.fn = NA,
  verbose = TRUE,
  call.rate = 1,
  cores = 1
)

Arguments

vcf.fn

vector of paths to genotype files in VCF format

annotations

data.frame with mapping of all samples names, ancestries and gender

out.dir

Path to output folder

model.name

Name of the output model

bed.fn

path to BED file with regions of interest

verbose

Print detailed information

call.rate

SNPs call rate cutoff for inclusion in the final reference model

cores

How many parallel cores to use in the reference model generation

Value

Logical value indicating the success of the analysis


List the models available

Description

This function prints the list of all available models.

Usage

getModelsList()

Value

data.frame of all available models to use with specified assembly and population


List the samples annotation

Description

This function prints the list of all 1,000 Genomes Project samples used to build the reference models.

Usage

getSamplesInfo()