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