[GenABEL-dev] descriptives.trait Patch
Yurii Aulchenko
yurii.aulchenko at gmail.com
Thu Mar 31 00:15:52 CEST 2011
Dear Nicola,
Many thanks for submitting this patch! These little problems were
pestering 'descriptive.traits' from the very moment the procedure was
invented -- so it is great news indeed and a great relief to have
these problems fixed!
I see no problem with applying this patch to the main release (and
within 5 days there were no concerns from others). So, I will apply
this patch + add RUnit regression tests for these three bugs -- and
when the commit (or any problems) will be there you will hear about
this on the mailing list.
best wishes,
Yurii
On Fri, Mar 25, 2011 at 1:02 PM, <pirastu at burlo.trieste.it> wrote:
> Dear all,
>
> attached you can find a patch to fix the bugs described underneath. To
> install from the root directory of /pkg: patch -p0 <
> patch_descriptives.trait.
>
> Best
>
> Nicola
>
> Patch for bugs #1184 #1185 #1259
>
> Bug [#1184] descriptives.trait can not see the variable in by.var argument
> unless full path specified
>
> Description:
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1184&group_id=505&atid=2058
>
> Changes: now by.var can be specified aslo as :"var_name" or ~var_name
>
> Test:
>
>> library(GenABEL)
>> data(ge03d2ex)
>> descriptives.trait(ge03d2ex,by.var="sex")
> No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw
> id 64 NA NA 72 NA NA NA NA
> sex 64 NA NA 72 NA NA NA NA
> age 64 46.942 12.479 72 50.959 13.107 0.070 0.081
> dm2 64 0.547 0.502 72 0.708 0.458 0.053 0.052
> height 64 162.680 6.819 71 175.534 7.943 0.000 0.000
> weight 64 78.605 26.908 71 95.322 21.441 0.000 0.000
> diet 64 0.109 0.315 72 0.014 0.118 0.025 0.019
> bmi 64 29.604 9.506 71 30.930 6.547 0.352 0.040
> Pexact
> id NA
> sex NA
> age NA
> dm2 0.074
> height NA
> weight NA
> diet 0.026
> bmi NA
>> descriptives.trait(ge03d2ex,by.var=~sex)
> No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw
> id 64 NA NA 72 NA NA NA NA
> sex 64 NA NA 72 NA NA NA NA
> age 64 46.942 12.479 72 50.959 13.107 0.070 0.081
> dm2 64 0.547 0.502 72 0.708 0.458 0.053 0.052
> height 64 162.680 6.819 71 175.534 7.943 0.000 0.000
> weight 64 78.605 26.908 71 95.322 21.441 0.000 0.000
> diet 64 0.109 0.315 72 0.014 0.118 0.025 0.019
> bmi 64 29.604 9.506 71 30.930 6.547 0.352 0.040
> Pexact
> id NA
> sex NA
> age NA
> dm2 0.074
> height NA
> weight NA
> diet 0.026
> bmi NA
>
> Bug [#1185] descriptives.trait with missings in by.var argument
>
> Description:
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1185&group_id=505&atid=2058
>
> Fixed: now by.var argument acceptes missing
>
> Test:
>
>> phdata(ge03d2ex)$sex[2] <- NA
>> descriptives.trait(ge03d2ex,by.var=phdata(ge03d2ex)$sex)
> No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw
> id 63 NA NA 72 NA NA NA NA
> sex 63 NA NA 72 NA NA NA NA
> age 63 47.003 12.570 72 50.959 13.107 0.076 0.088
> dm2 63 0.540 0.502 72 0.708 0.458 0.045 0.044
> height 63 162.573 6.819 71 175.534 7.943 0.000 0.000
> weight 63 77.651 26.009 71 95.322 21.441 0.000 0.000
> diet 63 0.111 0.317 72 0.014 0.118 0.024 0.017
> bmi 63 29.306 9.277 71 30.930 6.547 0.250 0.025
> Pexact
> id NA
> sex NA
> age NA
> dm2 0.051
> height NA
> weight NA
> diet 0.025
> bmi NA
>
> Bug [#1259] descriptives.trait with by.var argument does not work
> (contributed by Richard Ahn)
>
> Description:
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1259&group_id=505&atid=2058
>
> Comments: The problem was that for one of the traits one of the categories
> had all missing data, this made descriptives.trait crush.
>
> Fixed: descriptives.trait does not crush anymore.
>
> Test:
>
> nicola at nicola-VirtualBox:~/Scrivania$ R -f test.R
> WARNING: ignoring environment value of R_HOME
>
> R version 2.11.1 (2010-05-31)
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>> library(GenABEL)
> Carico il pacchetto richiesto: MASS
> GenABEL v. 1.6-6 (February 24, 2011) loaded
>
> Installed GenABEL version (1.6-6) is not the same as stable
> version available from CRAN (1.6-5). Unless used intentionally,
> consider updating to the latest CRAN version. For that, use
> 'install.packages("GenABEL")', or ask your system administrator
> to update the package.
>
>> convert.snp.illumina(infile="test_markers", outfile="test.raw")
> Reading genotypes from file 'test_markers' ...
> Writing to file 'test.raw' ...
> ... done.
>> test = load.gwaa.data(pheno="test_phenos", geno="test.raw", force=T)
> ids loaded...
> marker names loaded...
> chromosome data loaded...
> map data loaded...
> allele coding data loaded...
> strand data loaded...
> genotype data loaded...
> snp.data object created...
> assignment of gwaa.data object FORCED; X-errors were not checked!
>> attach(phdata(test))
>> descriptives.trait(data=test, by = bt)
> Error in t.test.formula(ctrao ~ svar) :
> grouping factor must have exactly 2 levels
> Error in kruskal.test.default(c(6L, 32L, 35L, 33L, 52L, 25L), c(1L, 1L, :
> all observations are in the same group
> No(by.var=0) Mean SD No(by.var=1) Mean SD Ptt Pkw Pexact
> id 5 NA NA 6 NA NA NA NA NA
> sex 5 0.2 0.447 6 0.333 0.516 0.657 0.637 1
> age 0 NaN NA 6 30.500 14.977 NA NA NA
> bt 5 NA NA 6 NA NA NA NA NA
>>
>>
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