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2.23 NManova - Program Arguments

This program carries out an ANOVA nucleosome by nucleosome and report the p-values of the interaction term.

Short Long Description
–filter Filter the nucleosome alignment by removing regions with unexpected alignments
–update Update the binary files generated by NMalign
–extract Just extract the data used to perform the ANOVA
–no-probe-effect Do not include a probe effect into the model
-i –input The input directory containing alignment files
-c –config The input configuration fileT
-o –output The output directory
-d –seqid The name of the chromosome to focus on
-j –prb-coverage The minimal fraction of observed probes spanning the nucleosome (default is 0.5)
-k –prb-anova The minimal number of probes within the aligned nucleosome (default is 10)
-p –permut The number of permutations to do to compute the empirical p-value by permutations (default is 0)
-s –start The starting position on the chromosome (use with –extract)
-e –end The ending position on the chromosome (use with –extract)