lineagespot: lineagespot

In nikopech/lineagespot: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

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,
  file.out.index = Sys.Date(),
  print.out = FALSE
)

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
file.out.index	A string index that is going to be contained in the output file names
print.out	Logical value indicating if the produced table should be printed. Default value is FALSE.

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"),

                      voc = c("B.1.1.7", "B.1.617.2"))

head( results$lineage.report )

nikopech/lineagespot documentation built on Dec. 28, 2021, 12:15 a.m.