Description Usage Arguments Examples
Makes the contexts useable in katPoint(), mutDis.plot() and baseSpe.plot().
1 | mutSNP.input(mut.data, chr = "chr", pos = "pos", ref = "ref", alt = "alt", build = NULL, k = 10)
|
mut.data |
A data frame of mutation(SNV) file. |
chr |
Column name in the mutation file corresponding to the chromosome. |
pos |
Column name in the mutation file corresponding to the mutation position. |
ref |
Column name in the mutation file corresponding to the reference base. |
alt |
Column name in the mutation file corresponding to the alternate base. |
build |
Reference build for chromosome sizes. Can be hg18, hg19 or hg38. |
k |
'K'-mer bases of flanking sequence of mutated base [default: 10]. |
1 2 3 4 5 6 7 8 9 10 11 | library(KataegisPortal)
library(BSgenome)
library(BSgenome.Hsapiens.UCSC.hg19)
mutData <- "examples/mutData.txt"
mutData <- read.table(mutData, header = TRUE,sep = "\t",as.is = TRUE)
mutSNP = mutSNP.input(mut.data = mutData,
chr = "chr",
pos = "pos",
ref = "ref",
alt = "alt",
build = "hg19")
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