[GenABEL-dev] descriptives.trait Patch
pirastu at burlo.trieste.it
pirastu at burlo.trieste.it
Thu Mar 31 12:20:28 CEST 2011
Hi Yurii,
I was looking at the documentation changes you made, and I just wanted to
point out that another version of the command is:
descriptives.trait(srdta, by.var=~sex)
whithout "".
Have no idea if this is usefull, but anyways just to let you know it was
in there.
Best
Nicola
> 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)
>> Copyright (C) 2010 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
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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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>
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