read_report2: Read kraken or centrifuge-style report

In fbreitwieser/pavian: Visualize and analyze metagenomics classification results

Read kraken or centrifuge-style report

Description

Read kraken or centrifuge-style report

Usage

read_report2(
  myfile,
  collapse = TRUE,
  keep_taxRanks = c("D", "K", "P", "C", "O", "F", "G", "S"),
  min.depth = 0,
  filter_taxon = NULL,
  has_header = NULL,
  add_taxRank_columns = FALSE
)

Arguments

myfile	kraken report file
collapse	should the results be collapsed to only those taxRanks specified in keep_taxRanks?
keep_taxRanks	taxRanks to keep when collapse is TRUE
min.depth	minimum depth
filter_taxon	filter certain taxon names
has_header	if the kraken report has a header or not
add_taxRank_columns	if TRUE, for each taxRank columns are added

Value

report data.frame

fbreitwieser/pavian documentation built on Jan. 5, 2024, 1:43 a.m.