Init DNA # DNA x <- DNAString("actttGtag") is(x) ## [1] "DNAString" "XString" "XRaw" "XVector" "Vector" "Annotated" #转录 x %>% complement() %>% RNAString() -> rna # 反向互补 x.r <- reverseComplement(x) x.r ## 9-letter "DNAString" instance ## seq: CTACAAAGT d <- DNAString("TTGAAAA-CTC-N") d ## 13-letter "DNAString" instance ## seq: TTGAAAA-CTC-N #subset subseq(x, start =1, end = 5) ## 5-letter "DNAString" instance ## seq: ACTTT #碱基置换 chartr(old = "A", new = "C", x) ## 9-letter "DNAString" instance ## seq: CCTTTGTCG #DNA_BASES DNA_BASES ## [1] "A" "C" "G" "T" #IUPAC_CODE_MAP IUPAC_CODE_MAP ## A C G T M R W S Y K ## "A" "C" "G" "T" "AC" "AG" "AT" "CG" "CT" "GT" ## V H D B N ## "ACG" "ACT" "AGT" "CGT" "ACGT" RNA x <- RNAString("acuuuGuag") is(x) ## [1] "RNAString" "XString" "XRaw" "XVector" "Vector" "Annotated" # 逆转录 x %>% complement() %>% DNAString() ## 9-letter "DNAString" instance ## seq: TGAAACATC # 翻译 codons(x) ## Views on a 9-letter RNAString subject ## subject: ACUUUGUAG ## views: ## start end width ## [1] 1 3 3 [ACU] ## [2] 4 6 3 [UUG] ## [3] 7 9 3 [UAG] translate(x) ## 3-letter "AAString" instance ## seq: TL* #dna -> rna:T <-> U DNAString("actttGtag") %>% RNAString() ## 9-letter "RNAString" instance ## seq: ACUUUGUAG #rna -> dna:U <-> T rna %>% DNAString() ## 9-letter "DNAString" instance ## seq: TGAAACATC AA: Amino acid x <- AAString("actttGtag") is(x) ## [1] "AAString" "XString" "XRaw" "XVector" "Vector" "Annotated" reads # all kmer reads <- mkAllStrings(c("A", "C", "G", "T"), 6) is(reads) ## [1] "character" "vector" "data.
