mapMutations: Map mutations on consensus sequence

In ste-depo/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Map mutations on consensus sequence

Description

mapMutations is a method for the class LowMACA that re-maps the mutations on a sequence to the relative position in a consensus sequence.

Usage

mapMutations(object)

Arguments

object

an object of class LowMACA

Details

Every position in the consensus alignement correspond to different positions in the single aligned sequences. The mutations are mapped according to this scheme that can be evinced from the slot alignment. mapMutations must be called after alignSequences and getMutations

Value

An object of class LowMACA with an update in the slot mutations. mapMutations add a object named aligned of class matrix in this slot that represents the absolute number of mutations in each sequence/position in the consensus as a matrix.

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

getMutations alignSequences LowMACA-class

Examples

#Create an object of class LowMACA
lm <- newLowMACA(pfam="PF12906")
#Align the sequences, requires clustalo
## Not run: lm <- alignSequences(lm)
#Get mutations from the corresponding genes
## Not run: lm <- getMutations(lm)
#Map mutations on the consensus sequence
## Not run: lm <- mapMutations(lm)

ste-depo/LowMACA documentation built on Oct. 15, 2022, 11:53 p.m.