i have a problem when i use LDheatmap.
Rstudio reported an error: column 1 is not a genotype object
Please help me to solve this problem.
###LDheatmap in CHR1
CHR1.b.FT_drought <- subset(CHR_drought, CHR == 1 & BP <= 7000000 & BP >= 6400000)
dist_CHR1.b_FT_drought <- CHR1.b.FT_drought$BP
SNPname.CHR1.b <- CHR1.b.FT_drought$SNP
dim(CHR1.b.FT_drought)
[1] 49 190
CHR1.b.FT_drought <-CHR1.b.FT_drought[,c(5:189)]
colnames(CHR1.b.FT_drought) <- NULL
CHR1.b.FT_drought <- as.data.frame(t(CHR1.b.FT_drought), row.names = T)
colnames(CHR1.b.FT_drought) <- SNPname.CHR1.b
CHR1.b.FT_drought <- makeGenotypes(CHR1.b.FT_drought, method = as.genotype)
###ldhm
ldhm.CHR1.b.FT_drought <- LDheatmap(CHR1.b.FT_drought, genetic.distances = dist_CHR1.b_FT_drought, LDmeasure = "r",
-
add.map = TRUE, add.key = TRUE, flip = TRUE, color = heat.colors(12))
Error in LDheatmap(CHR1.b.FT_drought, genetic.distances = dist_CHR1.b_FT_drought, :
column 1 is not a genotype object
Here is my data
Dj03_15206647F | Sj03_15208644R | Dj03_15208660R | Sj03_15215915R | Dj03_15224751R | Sj03_15224760F | Dj03_15290330R | |
---|---|---|---|---|---|---|---|
1 | AA | CC | TT | TT | AA | GG | AA |
2 | TT | GG | AA | TT | TT | AA | TT |
3 | TT | GG | AA | TT | TT | AA | TT |
4 | AA | CC | AA | AA | AA | GG | AA |
5 | AA | CC | AA | AA | AA | GG | AA |
6 | TT | GG | AA | TT | TT | AA | TT |