pavian (version 1.0.0)

read_report2: 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