FeatureExtract: Extracting sequence-based features.

In cma2015/RAP: Rank aggregation-based data fusion for gene prioritization

Description

This function generates sequence-based features from protein sequences using five scoring schemes.

Usage

  FeatureExtract(ProteinSeq, feature = c("AAC", "DAAC", "PAAC", "APAAC", "PCP"), 
                 lambda = 5, w = 0.05)

Arguments

ProteinSeq	A list of protein sequences.
feature	A vector of encoding schemes.
lambda	The lambda parameter for the PAAC and APAAC-related features, default is 5.
w	The weighting parameter for the PAAC and APAAC-related features, default is 0.05.

Value

A feature matrix with genes in rows, features in columns

Author(s)

Jingjing Zhai, Chuang Ma

Examples

  ## Not run: 
    
    ##generate a list of protein sequence
    exampleSeq1 <- "MVQYNFKRITVVPNGKEFVDIILSRTQRQTPTVVHKGYKINRLRQFYMRKVKYTQTNFHAKLSAIIDEFP"
    exampleSeq2 <- "MDSESESKLISFISQLVSRNNTDSENISCMIQTISLVSSMDLKSQPKPESKLMSLVTQTISLFNSM"
    featureMat <- FeatureExtract(ProteinSeq = list(exampleSeq1, exampleSeq2), feature = "AAC")
  
## End(Not run)

cma2015/RAP documentation built on Aug. 18, 2019, 8:02 p.m.