uniq_variants: uniq_variants

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

Description

Lineage report for variants overlapping

Usage

uniq_variants(
  hits_table = NULL,
  AF_threshold = 0.8,
  file.out = paste0("lineage_report_", Sys.Date(), ".txt"),
  print.out = FALSE
)

Arguments

hits_table	A tab-delimited table containing the identified overlaps/hits between the i nput files and the lineages' reports
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.
file.out	Given name for the output file
print.out	Logical value indicating if the produced table should be printed

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

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

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