merge_reports2: Merge report files into a wide format, with column(s) for...

In aroelo/ncp_pavian: Visualize and analyze metagenomics classification results

Description

Merge report files into a wide format, with column(s) for each report.

Usage

merge_reports2(
  my_reports,
  col_names = NULL,
  fix_taxnames = TRUE,
  update_progress = FALSE,
  id_cols = c("name", "taxRank", "taxID", "taxLineage"),
  numeric_cols = c("cladeReads", "taxonReads", "cladeIdentity", "taxonIdentity")
)

Arguments

my_reports	Report data.frames.
col_names	Column names.
fix_taxnames	Check if there are differences in the taxonomies of the reports.
update_progress	Update shiny progress
id_cols	Columns for taxdata
numeric_cols	Numeric data

Value

Combined data.frame

Examples

report_dir <- system.file("shinyapp", "example-data", "brain-biopsies", package="pavian")
reports <- read_reports(report_dir)

aroelo/ncp_pavian documentation built on May 2, 2021, 4:16 a.m.