featureAAindex(BioSeqClass)
featureAAindex()所属R语言包：BioSeqClass
Feature Coding by physicochemical/biochemical properties in AAindex
物化/生化特性的特征编码在AAindex
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Protein sequences are coded based on the physicochemical/biochemical properties of amino acids in AAindex database.
AAindex数据库中的氨基酸物化/生化特性的基础上，编码的蛋白质序列。
用法----------Usage----------
featureAAindex(seq,aaindex.name="all")
featureACI(seq,aaindex.name="all")
featureACF(seq,n,aaindex.name="all")
参数----------Arguments----------
参数：seq
a string vector for the protein, DNA, or RNA sequences.
为蛋白质，DNA或RNA序列的字符串向量。
参数：aaindex.name
a string for the name of physicochemical and biochemical properties in AAindx.
理化和生化特性AAindx名称的字符串。
参数：n
an integer used as paramter of featureACF (1<=n<=L-2, L is the the length of sequence). featureACF takes the auto-correlation between fragment X(1)...X(L-m) and X(m+1)...X(L) (1<=m<=n) as features.
featureACF放慢参数的整数（1 <= N <= l-2，L是序列的长度）。 featureACF x（1）片段。X（LM）和X（M +1）。X之间的自相关（长）（1 <= M <= N）为特征。
Details
详情----------Details----------
featureAAindex returns a matrix measuring the physicochemical and biochemical properties of amino acids by AAindex (http://www.genome.jp/aaindex). If parameter aaindex.name="all", all properties in AAindex will be considered, and each row represented the features of one sequence coding by a 531*N dimension numeric vector. If parameter aaindex.name is a name of property in AAindex, each row represented the features of one sequence coding by a N dimension numeric vector.
featureAAindex返回一个矩阵测量AAindex（http://www.genome.jp/aaindex）氨基酸的理化和生化特性。 ，如果参数aaindex.name =“所有”，在AAindex所有属性将被视为，每一行代表一个序列编码的功能，由一个531 * N维数字向量。如果参数aaindex.name是在AAindex财产的名称，每一行代表一个由N维数字向量编码序列的功能。
featureACI returns a matrix with 531 columns, measuring the average cumulative value of AAindex. N is the length of input sequence, and N must be odd. Central residue of all windows are the central residue of input sequence. Each column is the average cumulative AAindex over a sliding window.
featureACI531列返回一个矩阵，测量的平均AAindex累计值。 N是输入序列的长度，N必须是奇数。中央残留的所有窗口的输入序列的中央残留。每一列是通过滑动窗口累积平均AAindex。
featureACF returns a matrix with 531*n columns, measuring the Auto-Correlation Function (ACF) of AAindex. If parameter aaindex.name is a name of property in AAindex, each row represented the features of one sequence coding by a n dimension numeric vector.
featureACF返回531 * n列的矩阵，测量自相关函数的AAindex（ACF）。如果参数aaindex.name是在AAindex财产的名称，每一行代表一维数字向量编码序列的功能。
作者（S）----------Author(s)----------
Hong Li
举例----------Examples----------
if(interactive()){
file = file.path(.path.package("BioSeqClass"), "example", "acetylation_K.pos40.pep")
seq = as.matrix(read.csv(file,header=F,sep="\t",row.names=1))[,1]
AI_all = featureAAindex(seq)
AI_ANDN920101 = featureAAindex(seq,"ANDN920101")
ACI_all = featureACI(seq)
ACI_ANDN920101 = featureACI(seq,"ANDN920101")
ACF_all_1 = featureACF(seq,1)
ACF_ANDN920101_3 = featureACF(seq,3,"ANDN920101")
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-2-25 13:41:04
