sanity_check: Import the metadata and check it is correct

In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Description

Import the metadata and check it is correct

Usage

sanity_check(sample.info, reference = NULL, species = c("human",
  "mouse"), output.dir, threads = NULL)

Arguments

sample.info	character string giving the path to a tab-delimited text file with at least the columns <condition> (treatment condition), <sample> (sample name), and <file1> (absolute or relative path to the fastq files). If fastq files and PE reads, then a column <file2> should also be present. If a batch effect is to be included in the design, then this should be identified under the column <batch>. If IP controls are used then these should be specified in columns <input1> (and <input2> if paired reads); this is not necessary for ATAC-seq.
reference	character vector specifying the conditions in order. For example, c("A", "B", "C", "D") would mean "A" is the reference condition to which "B", "C" and "D" are compared; in addition, "C" and "D" will be compared to "B", and "D" will be compared to "C". If NULL then the comparisons will be arranged alphabetically. [DEFAULT = NULL].
species	character string specifying the name of the species. Only 'human', and 'mouse' are supported at present. [DEFAULT = human].
output.dir	character string specifying the directory to which results will be saved. If the directory does not exist, it will be created.
threads	an integer value indicating the number of parallel threads to be used by FastQC. [DEFAULT = maximum number of available threads - 1].

Value

A data.frame

anilchalisey/chompR documentation built on May 9, 2019, 3:59 a.m.