Description Usage Arguments Details Value
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 |
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 |
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.
Files are returned: deseq_results.txt
, class_results.txt
,
beneficial_counts.txt
, lethal_counts.txt
.
For usage, check out test file.
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