A Tool to Associate FASTA Sequences and Features

Documentation for package ‘SeqFeatR’ version 0.3.1

assocpair	Finding pairs of alignment positions that jointly mutate
assocpairfeat	Finding pairs of sequence alignment positions associated with sequence feature.
assocpoint	Searches for associations of single alignment positions with feature(s)
assocpointhierarchical	Searches for associations of single alignment positions with feature(s) with a simple hierarchical model
assocpointpair	Compare results of SeqFeatRs assocpoint with SeqFeatRs assocpair, assocpairfeat
assoctuple	Searches for associations of a tuple of alignment positions with feature(s)
comparewithancestral	Compares ancestral sequence with sequence alignment
foundereffectfinder	Tries to identify a founder effect in results from SeqFeatRs assocpair
getfreqs	Get frequencies for amino acids/nucleotides in alignment window (epitope)
orPlot	Visualize odds ratios and p-values from SeqFeatRs assocpoint
qvalues	Calculate q-values from p-values
rewritetuple	Rewrite result from SeqFeatRs assoctuple
SeqFeatR_GUI	GUI for SeqFeatR
smallmanhattan	A small version of manhattan plot
tartan	Visualize association of mutation pairs and features from two (comparable) analyses.
visualizepair	Visualize pairs of alignment positions that jointly mutate
visualizepairfeat	Visualize pairs of sequence alignment positions associated with sequence feature.
volcanoplot	Create volcano plot