run.read.MDscan: Run and read MDscan on training

In MEET: MEET: Motif Elements Estimation Toolkit

Description

This function runs and reads MDscan on training mode.

Usage

run.read.MDscan(input, k, len_motif, num_motif,call.MDscan)

Arguments

input	DNA sequence
k	Length DNA candidate seqeunce
len_motif	Length motif
num_motif	Number motif
call.MDscan	Path MDscan

Details

This function needs seqinr-Package and MDscan software.

Author(s)

Erola Pairo <[e-mail]> and Joan Maynou <[e-mail]>

References

X. S. Liu, D. L. Brutlag, and J. S. Liu, An algorithm for finding proteindna binding sites with applications to chromatin-immunopre- cipitation microarray experiments, Nat. Biotechnol. vol. 20, no. 8, pp. 835, Aug. 2002 [Online]. Available: http://dx.doi.org/10.1038/ nbt717

See Also

MEET, kfold.PredictInformationTheory, MEME, kfold.PredictDivergence, kfold.PCA

Examples

data(iicc)
#run.read.MDscan(input=iicc$DNA,k=length(iicc$DNA),len_motif=c(10,11,12), num_motif=2, call.MDscan)

MEET documentation built on May 2, 2019, 5:52 p.m.