CorMut (version 1.14.0)

filterSites-methods: filterSites methods

Description

filterSites implement filterSites methods for kaksCodon,kaksAA,ckaks and MI instances respectively.The functions filter the results of corresponding objects.

Methods

x = "kaksCodon"

filterSites(x,lod_cut = 2,freq_cut=0.01): Filter the results of kaksCodon object,two parameters are provided to control the output, lod_cut can assign an cutoff for lod confidence score to filter, and freq_cut assign the cutoff frequence of mutation, thus low-frequency mutations are ignored in the later analyses.

x = "kaksAA"

filterSites(x,lod_cut = 2,freq_cut=0.01): Filter the results of kaksAA object,two parameters are provided to control the output, lod_cut can assign an cutoff for lod confidence score to filter, and freq_cut assign the cutoff frequence of mutation, thus low-frequency mutations are ignored in the later analyses.

x = "ckaks"

filterSites(x,lod_cut=2): Filter the results of ckaks object,lod_cut can assign an cutoff for lod confidence score to filter.

x = "MI"

filterSites(x,p_cut=0.05): Filter the results of MI object,p_cut can assign an p value cutoff to filter the correlated mutations.

x = "JI"

filterSites(x,p_cut=0.05): Filter the results of MI object,p_cut can assign an p value cutoff to filter the correlated mutations.

See Also

kaksCodon, kaksAA, ckaksCodon, ckaksAA,miCodon,miAA,plot-methods

Examples

examplefile=system.file("extdata","PI_treatment.aln",package="CorMut")
example=seqFormat(examplefile)
result=kaksCodon(example)
resultfilter=filterSites(result)