read_pathoscope: Read Pathoscope output

In gwcbi/MetaOmicSet:

Description

Read Pathoscope output

Usage

read_pathoscope(dir_file = ".", s_list = NULL,
  smeta_file = "sample_metadata.csv", is.dir = 1, pattern0 = "",
  pattern1 = ".tsv", splitPoint = "[.]")

Arguments

dir_file	path for the directory with all sample files
s_list	a list of all the sample IDs involved in the experiment
smeta_file	a csv/tsv file containing the sample meta data
is.dir	a flag parameter, if the "dir_file" parameter is a directory(1) or a file (0)
pattern0	& pattern1 these are the pattern of strings before and after the sample IDs
splitPoint	the character that is used to split words in file names

Value

A list of "Count data matrix" and "Sample metadata data frame" and the "TaxIDs for the OTUs"

gwcbi/MetaOmicSet documentation built on May 20, 2019, 5:21 p.m.