check_sample: Check that targets file contains the necessary info in the...

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

Description

Check that targets file contains the necessary info in the right format

Usage

check_sample(sample.info, reference = 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].

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