Package 'lineagespot'

Title: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Description: Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.
Authors: Nikolaos Pechlivanis [aut, cre] , Maria Tsagiopoulou [aut], Maria Christina Maniou [aut], Anastasis Togkousidis [aut], Evangelia Mouchtaropoulou [aut], Taxiarchis Chassalevris [aut], Serafeim Chaintoutis [aut], Chrysostomos Dovas [aut], Maria Petala [aut], Margaritis Kostoglou [aut], Thodoris Karapantsios [aut], Stamatia Laidou [aut], Elisavet Vlachonikola [aut], Aspasia Orfanou [aut], Styliani-Christina Fragkouli [aut], Sofoklis Keisaris [aut], Anastasia Chatzidimitriou [aut], Agis Papadopoulos [aut], Nikolaos Papaioannou [aut], Anagnostis Argiriou [aut], Fotis E. Psomopoulos [aut]
Maintainer: Nikolaos Pechlivanis <[email protected]>
License: MIT + file LICENSE
Version: 1.9.0
Built: 2024-06-30 06:14:20 UTC
Source: https://github.com/bioc/lineagespot

Help Index

get_lineage_report

Description

Retrieve information about lineages' variants vie outbreak.info's API

Usage

get_lineage_report(
  lineages,
  base.url = "https://api.outbreak.info/genomics/lineage-mutations?pangolin_lineage="
)

Arguments

lineages

a character vector containing the names of the lineages of interest
base.url

The base API URL used to search for lineage reports Default value is "https://api.outbreak.info/genomics/ lineage-mutations?pangolin_lineage="

Value

A list of data table elements of lineage reports

Examples

get_lineage_report(lineages = c("B.1.1.7", "B.1.617.2"))

is_gff3

Description

Identify whether a file is in GFF3 format.

Usage

is_gff3(file)

Arguments

file

Path to GFF3 file.

Value

result; TRUE if the input file is in GFF3 format, FALSE if not.

Examples

gff3_path <- system.file("extdata", "NC_045512.2_annot.gff3",
  package = "lineagespot"
)
is_gff3(gff3_path)

lineagespot

Description

Identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s)

Usage

lineagespot(
  vcf_fls = NULL,
  vcf_folder = NULL,
  gff3_path = NULL,
  ref_folder = NULL,
  voc = c("B.1.617.2", "B.1.1.7", "B.1.351", "P.1"),
  AF_threshold = 0.8
)

Arguments

vcf_fls

A character vector of paths to VCF files
vcf_folder

A path to a folder containing all VCF files that will be integrated into a single table
gff3_path

Path to GFF3 file containing SARS-CoV-2 gene coordinates.
ref_folder

A path to a folder containing lineage reports
voc

A character vector containing the names of the lineages of interest
AF_threshold

A parameter indicating the AF threshold for identifying variants per sample

Value

A list of three elements;

  • Variants' table; A data table containing all variants that are included in the input VCF files

  • Lineage hits; A data table containing identified hits between the input variants and outbreak.info's lineage reports

  • Lineage report; A data table with computed metrics about the prevalence of the lineage of interest per sample.

Examples

results <- lineagespot(
    vcf_folder = system.file("extdata", "vcf-files",
        package = "lineagespot"
    ),
    gff3_path = system.file("extdata",
        "NC_045512.2_annot.gff3",
        package = "lineagespot"
    ),
    ref_folder = system.file("extdata", "ref",
        package = "lineagespot"
    )
)

head(results$lineage.report)

lineagespot_hits

Description

Find overlapping variants with SARS-CoV-2 reference lineages coming from outbreak.info reports

Usage

lineagespot_hits(
  vcf_table = NULL,
  ref_folder = NULL,
  voc = c("B.1.617.2", "B.1.1.7", "B.1.351", "P.1")
)

Arguments

vcf_table

A tab-delimited table containing all variants for all samples. This input is generated by the merge_vcf function.
ref_folder

A path to lineages' reports
voc

A character vector containing the names of the lineages of interest

Value

A data table containing all identified SARS-CoV-2 variants based on the provided reference files

Examples

variants_table <- merge_vcf(
    vcf_folder = system.file("extdata",
        "vcf-files",
        package = "lineagespot"
    ),
    gff3_path = system.file("extdata",
        "NC_045512.2_annot.gff3",
        package = "lineagespot"
    )
)

# retrieve lineage reports using outbreak.info's API

# use user-specified references
lineage_hits_table <- lineagespot_hits(
    vcf_table = variants_table,
    ref_folder = system.file("extdata", "ref",
        package = "lineagespot"
    )
)

list_input

Description

Check the validity of input parameters from lineagespot function.

Usage

list_input(vcf_fls = NULL, vcf_folder = NULL, gff3_path = NULL)

Arguments

vcf_fls

A character vector of paths to VCF files.
vcf_folder

A path to a folder containing all VCF files that will be integrated into a single table.
gff3_path

Path to GFF3 file containing SARS-CoV-2 gene coordinates.

Value

Return a character vector of paths to VCF files.

Examples

vcflist <- list_input(
  vcf_folder = system.file("extdata", "vcf-files",
    package = "lineagespot"
  ),
  gff3_path = system.file("extdata",
    "NC_045512.2_annot.gff3",
    package = "lineagespot"
  )
)

list_vcf

Description

Identify VCF files from a group of files.

Usage

list_vcf(vcf_fls = NULL, vcf_folder = NULL, gff3_path = NULL)

Arguments

vcf_fls

A character vector of paths to VCF files
vcf_folder

A path to a folder containing all VCF files that will be integrated into a single table
gff3_path

Path to GFF3 file containing SARS-CoV-2 gene coordinates.

Value

  • VCF list; A list where only VCF files are stored.

Examples

list_vcf_info <- list_vcf(
  vcf_folder = system.file("extdata", "vcf-files",
    package = "lineagespot"
  ),
  gff3_path = system.file("extdata",
    "NC_045512.2_annot.gff3",
    package = "lineagespot"
  )
)
print(list_vcf_info)

merge_vcf

Description

Merge Variant Calling Format (VCF) files into a single tab-delimited table

Usage

merge_vcf(vcf_fls = NULL, vcf_folder = NULL, gff3_path = NULL)

Arguments

vcf_fls

A list of paths to VCF files
vcf_folder

A path to a folder containing all VCF file that will be integrated into a single table
gff3_path

Path to GFF3 file

Value

A data table contaiing all variants from each sample of the input VCF files

Examples

merge_vcf(
    vcf_folder = system.file("extdata",
        "vcf-files",
        package = "lineagespot"
    ),
    gff3_path = system.file("extdata",
        "NC_045512.2_annot.gff3",
        package = "lineagespot"
    )
)

uniq_variants

Description

Lineage report for variants overlapping

Usage

uniq_variants(hits_table = NULL, AF_threshold = 0.8)

Arguments

hits_table

A tab-delimited table containing the identified overlaps/hits between the input files and the lineages' reports. This input is generated by the lineagespot_hits function.
AF_threshold

A parameter indicating the AF threshold that is going to applied in order to identify the presence or not of a variant. This is used to compute the number of variants in a sample and eventually the proportion of a lineage.

Value

A data table with metrics assessing the abundance of every lineage in each samples

Examples

variants_table <- merge_vcf(
    vcf_folder = system.file("extdata", "vcf-files",
        package = "lineagespot"
    ),
    gff3_path = system.file("extdata",
        "NC_045512.2_annot.gff3",
        package = "lineagespot"
    )
)

lineage_hits_table <- lineagespot_hits(
    vcf_table = variants_table,
    ref_folder = system.file("extdata", "ref",
        package = "lineagespot")
)

report <- uniq_variants(hits_table = lineage_hits_table)
head(report)