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comparison encode.R @ 2:f3f230290ffe draft

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author nicolas
date Fri, 21 Oct 2016 06:24:57 -0400
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1:c8ba405ffd13 2:f3f230290ffe
1 ########################################################
2 #
3 # creation date : 04/01/16
4 # last modification : 17/09/16
5 # author : Dr Nicolas Beaume
6 # owner : IRRI
7 #
8 ########################################################
9
10 log <- file(paste(getwd(), "log_encode.txt", sep="/"), open = "wt")
11 sink(file = log, type="message")
12
13 ############################ helper functions #######################
14
15 # encode one position in one individual
16 encodeGenotype.position <- function(x, major, code=c(0,1,2), sep=""){
17 res <- x
18 if(!is.na(x)) {
19 if(isHeterozygous(x, sep = sep)) {
20 # heterozygous
21 res <- code[2]
22 } else {
23 # determine whether it is the minor or major allele
24 x <- unlist(strsplit(x, sep))
25 # need to check only one element as we already know it is a homozygous
26 if(length(x) > 1) {
27 x <- x[1]
28 }
29 if(x==major) {
30 res <- code[3]
31 } else {
32 res <- code[1]
33 }
34 }
35 } else {
36 res <- NA
37 }
38 return(res)
39 }
40
41 # rewrite a marker to determine the major allele
42 encodeGenotype.rewrite <- function(x, sep=""){
43 res <- x
44 if(!is.na(x)) {
45 if(length(unlist(strsplit(x,sep)))==1) {
46 # in case of homozygous, must be counted 2 times
47 res <- c(x,x)
48 } else {
49 res <- unlist(strsplit(x, split=sep))
50 }
51 } else {
52 res <- NA
53 }
54 return(res)
55 }
56
57 # encode one individual
58 encodeGenotype.vec <- function(indiv, sep="", code=c(0,1,2)){
59 newIndiv <- unlist(lapply(as.character(indiv), encodeGenotype.rewrite, sep))
60 stat <- table(as.character(newIndiv))
61 major <- names(stat)[which.max(stat)]
62 indiv <- unlist(lapply(indiv, encodeGenotype.position, major, code, sep))
63 return(indiv)
64 }
65
66
67 isHeterozygous <- function(genotype, sep=""){
68 bool <- F
69 if(is.na(genotype)){
70 bool <- NA
71 } else {
72 x <- unlist(strsplit(genotype, sep))
73 if(length(x) > 1 & !(x[1] %in% x[2])) {
74 bool <- T
75 }
76
77 }
78 return(bool)
79 }
80
81 checkEncoding <- function(encoded, code=c(0,1,2)) {
82 check <- NULL
83 for(i in 1:ncol(encoded)) {
84 major <- length(which(encoded[,i]==code[3]))
85 minor <- length(which(encoded[,i]==code[1]))
86 if(major >= minor) {
87 check <- c(check, T)
88 } else {
89 check <- c(check, F)
90 }
91 }
92 return(check)
93 }
94
95 ################################## main function ###########################
96 # encode all individuals
97 # encode genotype into a {-1,0,1} scheme, where -1 = minor homozygous, 0 = heterozygous, 1 = major homozygous
98 encodeGenotype <- function(raw, sep="", code=c(0,1,2), outPath){
99 encoded <- apply(raw, 2, encodeGenotype.vec, sep, code)
100 encoded[is.na(encoded)] <- -1
101 write.table(encoded, file=paste(outPath,".csv", sep=""), row.names = F, sep="\t")
102 }
103
104 ############################ main #############################
105 # running from terminal (supposing the OghmaGalaxy/bin directory is in your path) :
106 # encode.sh -i path_to_raw_data -s separator -c code -o path_to_result_directory
107 ## -i : path to the file that contains the genotypes to encode, must be a .rda file (as outputed by loadGenotype.R).
108 # please note that the table must be called "genotype" when your datafile is saved into .rda (automatic if loadGenotype.R was used)
109
110 ## -s : in case of heterozygous both allele are encoded in the same "cell" of the table and separated by a character
111 # (most often "" or "/"). This argument specify which character
112
113 ## -c : the encoding of minor allele/heterozygous/major allele. by default {-1,0,1}
114
115 ## -o : path to the file of encoded genotype. the .rda extension is automatically added
116
117 cmd <- commandArgs(T)
118 source(cmd[1])
119 genotype <- read.table(genotype, sep="\t", stringsAsFactors = F, h=T)
120 # deal with optional argument
121 code <- strsplit(code, ",")
122 code <- unlist(lapply(code, as.numeric), use.names = F)
123 encodeGenotype(raw=genotype, sep=sep, code = code, outPath = out)
124 cat(paste(out,".csv", "\n", sep=""))