doDE: Make differential expression analysis
In genialis/shRNAde: Functions needed to support the shRNA pipeline in rewolwe-bio

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

1	doDE(input, sample_list = NULL)

`input`	Character. A relative or absolute path to a parameters file. See Details.
`sample_list`	Character. Vector of aboslute or relative paths to sample expressions. See `importExpressionData` for more info. If omitted, `./data` is searched for `.txt` files.

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.

For usage, check out test file.

genialis/shRNAde documentation built on Dec. 11, 2018, 1:34 a.m.