FactorTransform: Metric Solution for Amino Acid characters
In HDMD: Statistical Analysis Tools for High Dimension Molecular Data (HDMD)

Description Usage Arguments Value Author(s) References See Also Examples

Based off the work done by Atchley et al 2005, Amino Acids are transformed into 5 metrics according to factor analysis scores representing Factor1 (PAH): Polarity, Accessibility, Hydrophobicity; Factor2 (PSS): Propensity for Secondary Structure; Factor3 (MS) : Molecular Size; Factor4 (CC): Codon Composition; Factor5 (EC): Electrostatic Charge. These numerics provide a biologically meaningful value that establishes a platform capable of handling rigorous statistical techniques such as analysis of variance, regression, discriminant analysis, etc.

1	FactorTransform(Source, Search = AminoAcids, Replace = AAMetric.Atchley, Factor = 1, bycol = TRUE, SeqName = NULL, alignment=FALSE, fillblank=NA)

`Source`	Vector, Matrix or List of Amino Acid Sequences using the single character abbreviation~
`Search`	Vector of symbols to search over. Default is the list of Amino Acids.
`Replace`	Vector or Matrix of values to replace Search items. Rows of Replace correspond to elements of Search when byCol = TRUE.
`Factor`	If Replace is a matrix, Factor designates which vector of Replace is used.
`bycol`	logical. Designates if Replace is oriented so that columns correspond to replaceable elements
`SeqName`	Vector of sequence names
`alignment`	if FALSE, result is a list. If TRUE result is a matrix and hanging rows are filled with fillblank
`fillblank`	if alignment is TRUE, trailing sites are filled with this value. Default is NA, but can be numeric.

A list or matrix containing numeric representations of the sequences is returned. If alignment is FALSE, each sequence is a new element in the list containing a vector of values with length corresponding to the length of the original sequence. If alignment is TRUE, a matrix is returned with each row representing a sequence metric. If the sequence lengths were unequal, trailing blanks are specified by the fillblank parameter.

Lisa McFerrin

Atchley, W. R., Zhao, J., Fernandes, A. and Drueke, T. 2005. Solving the sequence "metric" problem: Proc. Natl. Acad. Sci. USA 102: 6395-6400.

lapply, replace

FactorTransform("HDMD", Replace= AAMetric.Atchley)

data(bHLH288)
bHLH_Seq = as.vector(bHLH288[,2])
bHLH_ccList = FactorTransform(bHLH_Seq, Factor=4)
bHLH_ms     = FactorTransform(bHLH_Seq, Factor=3, alignment=TRUE)

bHLH_ms[c(20:25, 137:147, 190:196, 220:229, 264:273),1:8]