conservityTable: This function calculates the conservity of all positions for...

In hezijin/conservedPos: Use conservedPos find important conserved sites for small target region

Description

This function calculates the conservity of all positions for input sequences and generate a vector contains each position's conservity

Usage

conservityTable(seqSet)

Arguments

seqSet

seqSet A set of aligned sequence read from fasta file

Value

a vector contains each position's highest frequency

Examples

# Example 1 : Create conservity Table for testSeqShort.
data(testSeqShort)
testSeq <- testSeqShort
table  <- conservityTable(testSeq)
# You will see a vector containing 37 numbers (max length), these numbers are
# the highest frequency for each position.
table

# Example 2: Create conservity Table for another sequence set, a raw data
# sampleSeq3.txt. This should takes longer time to run.
findpath <- system.file("extdata", "sampleSeq3.txt", package = "conservedPos")
rawSeq <- Biostrings::readBStringSet(findpath,"fasta")
table <- conservityTable(rawSeq)
# Should have 140 numbers(max length of rawSeq), and
# each number is the the highest frequency for each position
table

hezijin/conservedPos documentation built on Jan. 1, 2021, 3:18 a.m.