Dear All,
I am trying to plot manhattan plot , I first tried with qqplot , it looked like a scatter plot and very funny> plotGrandLinear(MPB, aes(y = P), color = c("#7fc97f", "#fdc086"))
Error: Objects of type data.frame not supported by autoplot. Please use qplot() or ggplot() instead
> str(MPB)
'data.frame': 63 obs. of 4 variables:
$ CHR: num 1 1 1 1 1 1 1 1 1 1 ...
$ SNP: chr "rsID0" "rsID1" "rsID2" "rsID3" ...
$ BP : num 1310924 16840541 16840567 16840575 17231444 ...
$ P : num 1 0.822 0.001 0.807 0 0.357 0.148 0.95 1 0.22 ..
> makeGRangesFromDataFrame(MPB,keep.extra.columns=FALSE,ignore.strand=FALSE,seqinfo=NULL,seqnames.field=c("CHR","SNP","BP","P"),start.field=c("start","CHR"),end.field=c("end","P"))
Error in .find_seqnames_col(df_colnames0, seqnames.field0, prefix) :
cannnot determine seqnames column unambiguously
> gr1 <- makeGRangesFromDataFrame(MPB, keep.extra.columns=TRUE,
+ starts.in.df.are.0based=TRUE, start=1, end=23)
Error in .normarg_field(start.field, "start") :
'start.field' must be a character vector with no NAs
> gr1 <- makeGRangesFromDataFrame(MPB, keep.extra.columns=TRUE,
+ starts.in.df.are.0based=TRUE)
Error in .find_start_end_cols(df_colnames0, start.field0, end.field0) :
cannnot determine start/end columns
It is still giving me error
as I attached my data( This is how my data looks) , Thanks so much again.
CHR |
SNP |
BP |
P |
|
1 |
1 |
rsID0 |
1310924 |
1.000 |
2 |
1 |
rsID1 |
16840541 |
0.822 |
3 |
1 |
rsID2 |
16840567 |
0.001 |
4 |
1 |
rsID3 |
16840575 |
0.807 |
5 |
1 |
rsID4 |
17231444 |
0.000 |
6 |
1 |
rsID5 |
26758773 |
0.357 |
7 |
1 |
rsID6 |
40506239 |
0.148 |
8 |
1 |
rsID7 |
47779951 |
0.950 |
9 |
1 |
rsID8 |
109289236 |
1.000 |
10 |
1 |
rsID9 |
110881432 |
0.220 |