[R] issue with numeric

[Ana Marija]

Hello,

the error was in the code:
D = read.table(opt_input, head = FALSE, stringsAsFactors = FALSE)

I should have there header=TRUE

Sorry for bothering with this,

Ana

On Wed, Dec 18, 2019 at 2:44 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> Hi Ivan,
>
> here it is:
>
> > str(a)
> 'data.frame':    17389 obs. of  21 variables:
>  $ V1             : Factor w/ 17389 levels "ENSG00000000419",..: 14093
> 14622 14705 14651 14784 17138 14773 14163 14569 15156 ...
>  $ V2             : Factor w/ 22 levels "chr1","chr10",..: 1 1 1 1 1 1
> 1 1 1 1 ...
>  $ V3             : int  29571 36082 91106 133724 173863 200323 259025
> 297503 348367 493242 ...
>  $ V4             : int  29570 36081 91105 133723 173862 200322 259024
> 297502 348366 493241 ...
>  $ V5             : Factor w/ 2 levels "-","+": 1 1 1 1 1 1 1 1 1 1 ...
>  $ V6             : int  983 1006 1169 1340 1441 1620 1897 2032 2175 2697 ...
>  $ V7             : int  -828479 -38709 -782443 69986 -831895 -980529
> -647609 -946918 -631093 -886444 ...
>  $ V8             : Factor w/ 17104 levels "1:10095977:G:GT",..: 7339
> 4761 2344 7480 12580 4781 14856 3061 9397 6938 ...
>  $ V9             : Factor w/ 22 levels "chr1","chr10",..: 1 1 1 1 1 1
> 1 1 1 1 ...
>  $ V10            : int  858049 74790 873548 63735 1005757 1180851
> 906633 1244420 979459 1379685 ...
>  $ V11            : int  858049 74790 873548 63738 1005771 1180851
> 906633 1244420 979459 1379685 ...
>  $ Effect_allele  : Factor w/ 358 levels "A","AAAAACAAAAC",..: 267 190
> 92 92 54 92 190 1 267 267 ...
>  $ Baseline_allele: Factor w/ 435 levels "A","AAAAAAAAAATAAAAAT",..:
> 112 112 325 175 1 325 325 237 112 237 ...
>  $ V12            : int  404 404 404 404 404 404 404 404 404 404 ...
>  $ V13            : num  348 347 347 339 342 ...
>  $ V14            : num  1.04 1.03 1.02 1.04 1.04 ...
>  $ V15            : num  140 138 153 154 171 ...
>  $ V16            : num  0.000742 0.002822 0.000626 0.000798 0.002894 ...
>  $ V17            : num  0.269 -0.687 -0.285 -0.398 0.341 ...
>  $ V18            : num  0.196 0.531 0.203 0.265 0.639 ...
>  $ V19            : num  0.198 0.529 0.199 0.261 0.634 ...
>
> and this:
>
> > which(is.na(as.numeric(as.character(a[,18]))))
>  [1] 10757 11062 11063 11064 11065 11066 11067 11068 11069 11070 11071 11072
> [13] 11073 11074 11075
> > which(is.na(as.numeric(as.character(a[,19]))))
>  [1] 10757 11062 11063 11064 11065 11066 11067 11068 11069 11070 11071 11072
> [13] 11073 11074 11075
>
> columns 18 and 19 seems to be numeric, what is could be the issue?
>
> On Wed, Dec 18, 2019 at 1:49 PM Ivan Krylov <krylov.r00t using gmail.com> wrote:
> >
> > On Wed, 18 Dec 2019 12:25:24 -0600
> > Ana Marija <sokovic.anamarija using gmail.com> wrote:
> >
> > > Error in cor(D[, 18 + exon_offset], D[, 19 + exon_offset]) :
> > >   'x' must be numeric
> >
> > Try str(a) to find out the types of the columns. A stray typo could
> > make a representation of a number impossible to parse and make the
> > whole column textual. Use
> > which(is.na(as.numeric(as.character(a[,column_number])))) to find out
> > the row number where it happened (using extra as.character() here in
> > case the column is a factor).
> >
> > --
> > Best regards,
> > Ivan