doDE: Make differential expression analysis

Description Usage Arguments Details Value

Description

Input a set of count matrices, define relationships and perform a differential analysis. Return several outputs, including differentil expression result and some extra comparisons.

Usage

1
doDE(input, sample_list = NULL)

Arguments

input

Character. A relative or absolute path to a parameters file. See Details.

sample_list

Character. Vector of absolute or relative paths to sample expressions or folder containing sample expressions. See importExpressionData for more info.

Details

input file should be an excel (xlsx) file with tabs sample_key, contrasts, overall_contrasts and classification_parameters. sample_key should have columns sample, <variables> (depends on the experiment) and replicate. contrasts should have columns group_1 and group_2, and they should hold which groups to test against each other. Sheet overall_contrasts should have groups of overall contrasts in columns, where rows represent pairs of comparisons. classification_parameters sheet should have twothree columns, threshold, value and description. See sample file for details.

Value

Files are returned: deseq_results.txt, class_results.txt, beneficial_counts.txt, lethal_counts.txt. For usage, check out test file.


genialis/shRNAde documentation built on May 3, 2019, 7:39 p.m.