[R] problem with factor levels

[PIKAL Petr]

Hi

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Jeremy.Shearman
> Sent: Tuesday, December 04, 2012 9:35 AM
> To: r-help at r-project.org
> Subject: [R] problem with factor levels
> 
> Hi
>       I have a data.frame with 371,718 obs. of 12 variables (see below
> for an str). My problem is with V1, a Factor w/ 93144 levels, there
> should actually be 93994 levels. Each entry looks like:
> comp[number]_c[number]_seq[number]
> for example
> comp215489_c0_seq40
> R is grouping as though the last number is a decimal for some reason,
> in other words comp215489_c0_seq40 and comp215489_c0_seq4 are
> considered to be the same. My problem is that they are not the same so
> when I group by this factor I am losing 800 levels.
> 

Hm. How did you constructed those factors?

> factor(c("comp215489_c0_seq40", "comp215489_c0_seq4") )
[1] comp215489_c0_seq40 comp215489_c0_seq4 
Levels: comp215489_c0_seq4 comp215489_c0_seq40

gives me 2 levels as expected. I also doubt that R will do such stripping during reading from other file.

Regards
Petr


> Here is an str
> 
> 'data.frame':	371718 obs. of  12 variables:
>  $ V1 : Factor w/ 93144 levels "comp100000_c0_seq1",..: 92271 91685 29
> 30
> 1564 1564 1623 91700 91701 91848 ...
>  $ V2 : Factor w/ 17162 levels "gi|345842331|ref|NM_001244016.1|",..:
> 10119
> 10779 13210 13210 11522 8115 13079 14493 14493 15858 ...
>  $ V3 : num  95.5 90.2 98.7 99.2 81.4 ...
>  $ V4 : int  335 153 237 122 258 127 306 258 120 177 ...
>  $ V5 : int  15 15 3 1 38 19 20 23 5 9 ...
>  $ V6 : int  0 0 0 0 4 2 0 0 0 0 ...
>  $ V7 : int  1 45 1 43 1 129 1 54 1 70 ...
>  $ V8 : int  335 197 237 164 254 254 306 311 120 246 ...
>  $ V9 : int  6866 18 3172 3438 67 122 3927 42 346 195 ...
>  $ V10: int  7200 170 3408 3559 318 247 4232 299 465 19 ...
>  $ V11: num  7e-155 2e-46 4e-125 2e-61 3e-24 ...
>  $ V12: num  545 184 446 234 111 69.9 448 329 198 280 ..
> 
> 
> 
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