read_tags: Interpret the files produced by my count_idx.pl script.
In abelew/stampr: Perform the STAMP analysis

read_tags

R Documentation

Interpret the files produced by my count_idx.pl script.

Description

This uses the index_table column in the metadata, reads this files associated with it, and creates some data structures with the results. These include a modified version of the metadata, containing some summary information, a table of the reads/tag observed, and a long table for ggplot.

Usage

read_tags(
  metadata,
  id_column = "sampleid",
  index_column = "index_table",
  sample_column = "replicate",
  output = NULL,
  cutoff = 3
)

Arguments

`metadata`	Sample metadata.
`id_column`	Column in the metadata containing the sample names.
`index_column`	Column in the metadata containing the tag tables.
`output`	Write out the matrix to this file (if provided).
`cutoff`	Initial reads/tag filter.