Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/504-extractProtMoreauBroto.R
Normalized Moreau-Broto Autocorrelation Descriptor
1 2 3 | extrProtMoreauBroto(x, props = c("CIDH920105", "BHAR880101", "CHAM820101",
"CHAM820102", "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"),
nlag = 30L, customprops = NULL)
|
x |
A character vector, as the input protein sequence. |
props |
A character vector, specifying the Accession Number of the target properties. 8 properties are used by default, as listed below:
|
nlag |
Maximum value of the lag parameter. Default is |
customprops |
A |
This function calculates the normalized Moreau-Broto
autocorrelation descriptor (Dim: length(props) * nlag
).
A length nlag
named vector
Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>
AAindex: Amino acid index database. http://www.genome.ad.jp/dbget/aaindex.html
Feng, Z.P. and Zhang, C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. Journal of Protein Chemistry, 19, 269-275.
Horne, D.S. (1988) Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers, 27, 451-477.
Sokal, R.R. and Thomson, B.A. (2006) Population structure inferred by local spatial autocorrelation: an Usage from an Amerindian tribal population. American Journal of Physical Anthropology, 129, 121-131.
See extrProtMoran
and extrProtGeary
for Moran autocorrelation descriptors and
Geary autocorrelation descriptors.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
extrProtMoreauBroto(x)
myprops = data.frame(AccNo = c("MyProp1", "MyProp2", "MyProp3"),
A = c(0.62, -0.5, 15), R = c(-2.53, 3, 101),
N = c(-0.78, 0.2, 58), D = c(-0.9, 3, 59),
C = c(0.29, -1, 47), E = c(-0.74, 3, 73),
Q = c(-0.85, 0.2, 72), G = c(0.48, 0, 1),
H = c(-0.4, -0.5, 82), I = c(1.38, -1.8, 57),
L = c(1.06, -1.8, 57), K = c(-1.5, 3, 73),
M = c(0.64, -1.3, 75), F = c(1.19, -2.5, 91),
P = c(0.12, 0, 42), S = c(-0.18, 0.3, 31),
T = c(-0.05, -0.4, 45), W = c(0.81, -3.4, 130),
Y = c(0.26, -2.3, 107), V = c(1.08, -1.5, 43))
# Use 4 properties in the AAindex database, and 3 cutomized properties
extrProtMoreauBroto(x, customprops = myprops,
props = c('CIDH920105', 'BHAR880101',
'CHAM820101', 'CHAM820102',
'MyProp1', 'MyProp2', 'MyProp3'))
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