Entering edit mode
3.9 years ago
monlawski
•
0
Hello everyone, im new to the r and i have some problems. I need to use just seqinr, so my question is ;
I need to read my genes in FASTA into the list genes so it should be like ;
library(seqinr)
genes <- read.fasta('geness.txt')
length(genes)
## [1] 4120
and i can see my number of genes with the length.
but I need to apply codon_count() to each gene and store the results in the list gene_codon_count.
codon_count <- function(gene) {
answer <- rep(0, 64)
names(answer) <- c("aaa", "aac", "aag", "aat", "aca", "acc", "acg", "act",
"aga", "agc", "agg", "agt", "ata", "atc", "atg", "att", "caa", "cac",
"cag", "cat", "cca", "ccc", "ccg", "cct", "cga", "cgc", "cgg", "cgt",
"cta", "ctc", "ctg", "ctt", "gaa", "gac", "gag", "gat", "gca", "gcc",
"gcg", "gct", "gga", "ggc", "ggg", "ggt", "gta", "gtc", "gtg", "gtt",
"taa", "tac", "tag", "tat", "tca", "tcc", "tcg", "tct", "tga", "tgc",
"tgg", "tgt", "tta", "ttc", "ttg", "ttt")
for(i in seq(from=1, to=length(gene), by=3)) {
codon <- tolower(paste0(gene[i], gene[i+1], gene[i+2]))
answer[codon] <- answer[codon] + 1
}
return(answer)
}
and the answer should be
length(genes_codon_count)
## [1] 4120
length(genes_codon_count[[1]])
## [1] 64
But i cant get any results so im missing or doing something wrong.