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Copy pathCodonInfoTables.R
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CodonInfoTables.R
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subTypeTable<-read.delim(file = "~/Research/CirSeq/ResSubTable_Pechmann2014.txt" , head = T)
rownames(subTypeTable)<-colnames(subTypeTable)
states=as.array(c('TTT', 'TTC', 'TTA', 'TTG',
'TCT', 'TCC', 'TCA', 'TCG',
'TAT', 'TAC', 'TAA', 'TAG',
'TGT', 'TGC', 'TGA', 'TGG',
'CTT', 'CTC', 'CTA', 'CTG',
'CCT', 'CCC', 'CCA', 'CCG',
'CAT', 'CAC', 'CAA', 'CAG',
'CGT', 'CGC', 'CGA', 'CGG',
'ATT', 'ATC', 'ATA', 'ATG',
'ACT', 'ACC', 'ACA', 'ACG',
'AAT', 'AAC', 'AAA', 'AAG',
'AGT', 'AGC', 'AGA', 'AGG',
'GTT', 'GTC', 'GTA', 'GTG',
'GCT', 'GCC', 'GCA', 'GCG',
'GAT', 'GAC', 'GAA', 'GAG',
'GGT', 'GGC', 'GGA', 'GGG', NA))
alphaVec<-c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y","X","U")
residues = c( "F","F","L","L",
"S","S","S","S",
"Y","Y","X","X",
"C","C","X","W",
"L","L","L","L",
"P","P","P","P",
"H","H","Q","Q",
"R","R","R","R",
"I","I","I","M",
"T","T","T","T",
"N","N","K","K",
"S","S","R","R",
"V","V","V","V",
"A","A","A","A",
"D","D","E","E",
"G","G","G","G", "U")
res3 = c( "PHE","PHE","LEU","LEU",
"SER","SER","SER","SER",
"TYR","TYR","XXX","XXX",
"CYS","CYS","XXX","TRP",
"LEU","LEU","LEU","LEU",
"PRO","PRO","PRO","PRO",
"HIS","HIS","GLN","GLN",
"ARG","ARG","ARG","ARG",
"ILE","ILE","ILE","MET",
"THR","THR","THR","THR",
"ASN","ASN","LYS","LYS",
"SER","SER","ARG","ARG",
"VAL","VAL","VAL","VAL",
"ALA","ALA","ALA","ALA",
"ASP","ASP","GLU","GLU",
"GLY","GLY","GLY","GLY", "UTR")
resCharacter=c('acidic',
'acyclic',
'aliphatic',
'aromatic',
'basic',
'buried',
'charged',
'cyclic',
'hydrophobic',
'large',
'medium',
'negative',
'neutral',
'polar',
'positive',
'small',
'surface',
'stop')
resList=c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "X")
resAnnotMatrix=##Binary Vector -- could be mproved to be continuous data, see K. Chou's stuff.
matrix(
#A R N D C E Q G H I L K M F P S T W Y V * U
c(0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,# acidic
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0,# acyclic
1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,# aliphatic
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0,# aromatic
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,# basic
1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0,# buried
0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,# charged
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0,# cyclic
1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0,# hydrophobic
0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0,# large
0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0,# medium
0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,# negative
1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0,# neutral
0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0,# polar
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,# positive
1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,# small
0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0,# surface
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0),# stop
byrow=T,ncol=22,dimnames = list(resCharacter,c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "X","U")))