Convertendo arquivos Rdata em CSV - Erro nos argumentos data.frame implica um número diferente de linhas
Estou tentando usar o código R desteresponda para converter um monte de arquivos rdata para CSV.
resave <- function(file){
e <- new.env(parent = emptyenv())
load(file, envir = e)
objs <- ls(envir = e, all.names = TRUE)
for(obj in objs) {
.x <- get(obj, envir =e)
message(sprintf('Saving %s as %s.csv', obj,obj) )
write.csv(.x, file = paste0(obj, '.csv'))
}
}
resave('yourData.RData')
No entanto, em um dos arquivos, estou recebendo este erro:
Error in data.frame(`2` = list(pos = c(6506L, 6601L, 21801L, 21811L, 21902L, :
arguments imply differing number of rows: 7670, 9729, 114, 2422
Calls: resave ... as.data.frame -> as.data.frame.list -> eval -> eval -> data.frame
Tentei procurar a mensagem de erro, mas não consigo realmente entender.
Esse arquivo rdata foi criado de forma inadequada?
Existe uma maneira melhor de converter arquivos Rdata arbitrários em CSV? (Não sei os nomes dos objetos nos arquivos com antecedência.)
Atualizar:
Aqui está o que estou vendo nesse arquivo rdata. Se é alguma ajuda ?? (Lembre-se de que não consigo editar os arquivos rdata, então estou tentando descobrir algo que os converta em CSV como estão.)
> load("indiv8-hmmprob.RData")
> ls()
[1] "dataa"
> write.csv(dataa, file="greg.csv")
Error in data.frame(`2` = list(pos = c(6506L, 6601L, 21801L, 21811L, 21902L, :
arguments imply differing number of rows: 7670, 9729, 114, 2422
> names(dataa)
[1] "2" "3" "4" "X"
> str(dataa)
List of 4
$ 2:'data.frame': 7670 obs. of 23 variables:
..$ pos : int [1:7670] 6506 6601 21801 21811 21902 21931 22487 24071 26674 26713 ...
..$ ref : chr [1:7670] "C" "A" "G" "A" ...
..$ cons : chr [1:7670] "T" "T" "A" "G" ...
..$ reads : chr [1:7670] "ttt" "tttt" "AAAAA" "GGGGG" ...
..$ quals : chr [1:7670] "FBB" "IIIB" "IFIII" "FFIII" ...
..$ A : int [1:7670] 0 0 5 0 0 0 1 0 0 1 ...
..$ C : int [1:7670] 0 0 0 0 0 0 0 0 2 0 ...
..$ G : int [1:7670] 0 0 0 5 11 0 0 0 0 0 ...
..$ T : int [1:7670] 3 4 0 0 0 10 0 2 0 0 ...
..$ N : int [1:7670] 0 0 0 0 0 0 0 0 0 0 ...
..$ bad : chr [1:7670] NA NA NA NA ...
..$ par1ref : chr [1:7670] "C" "A" "G" "A" ...
..$ par2ref : chr [1:7670] "T" "T" "A" "G" ...
..$ read : Factor w/ 8397 levels "1","2","3","4",..: 2 2 3 3 3 3 4 7 9 9 ...
..$ count : int [1:7670] 3 4 5 5 11 10 1 2 2 1 ...
..$ read_allele : chr [1:7670] "T" "T" "A" "G" ...
..$ Pr(y| par1/par1 ): num [1:7670] 9.30e-04 5.69e-04 3.47e-04 1.42e-04 1.90e-08 ...
..$ Pr(y| par1/par2 ): num [1:7670] 4.58e-02 1.64e-02 2.41e-03 4.09e-03 8.89e-07 ...
..$ Pr(y| par2/par2 ): num [1:7670] 1.61e-01 8.40e-02 8.94e-03 2.09e-02 3.29e-06 ...
..$ est : int [1:7670] 3 3 3 3 3 3 3 3 3 3 ...
..$ Pr( par1/par1 |y): num [1:7670] 4.67e-25 2.25e-27 1.98e-31 2.93e-32 2.82e-34 ...
..$ Pr( par1/par2 |y): num [1:7670] 2.95e-11 2.86e-11 2.49e-14 1.98e-14 1.08e-14 ...
..$ Pr( par2/par2 |y): num [1:7670] 1 1 1 1 1 ...
..- attr(*, "badpos")= int [1:11386] 21900 21905 22840 24029 27149 27170 28024 42187 46927 46990 ...
$ 3:'data.frame': 9729 obs. of 23 variables:
..$ pos : int [1:9729] 6001 22537 25304 27228 28817 28842 30540 48903 48938 48943 ...
..$ ref : chr [1:9729] "A" "A" "A" "C" ...
..$ cons : chr [1:9729] "A" "G" "T" "C" ...
..$ reads : chr [1:9729] "," "GGG" "TTTTT" "," ...
..$ quals : chr [1:9729] "F" "BBB" "BFFFF" "B" ...
..$ A : int [1:9729] 1 0 0 0 0 0 0 0 0 0 ...
..$ C : int [1:9729] 0 0 0 1 1 0 0 0 0 1 ...
..$ G : int [1:9729] 0 3 0 0 0 0 0 0 0 0 ...
..$ T : int [1:9729] 0 0 5 0 0 1 1 1 1 0 ...
..$ N : int [1:9729] 0 0 0 0 0 0 0 0 0 0 ...
..$ bad : chr [1:9729] NA NA NA NA ...
..$ par1ref : chr [1:9729] "A" "A" "A" "C" ...
..$ par2ref : chr [1:9729] "G" "G" "T" "T" ...
..$ read : Factor w/ 10640 levels "1","2","3","4",..: 1 3 4 5 7 7 8 10 10 10 ...
..$ count : int [1:9729] 1 3 5 1 1 1 1 1 1 1 ...
..$ read_allele : chr [1:9729] "A" "G" "T" "C" ...
..$ Pr(y| par1/par1 ): num [1:9729] 0.969856 0.002707 0.000372 0.969639 0.969856 ...
..$ Pr(y| par1/par2 ): num [1:9729] 0.48995 0.0567 0.00228 0.48988 0.48995 ...
..$ Pr(y| par2/par2 ): num [1:9729] 0.01005 0.26071 0.00798 0.01012 0.01005 ...
..$ est : int [1:9729] 1 3 3 1 1 1 1 3 1 3 ...
..$ Pr( par1/par1 |y): num [1:9729] 2.18e-10 2.82e-11 2.67e-11 2.65e-11 2.63e-11 ...
..$ Pr( par1/par2 |y): num [1:9729] 0.688 0.688 0.688 0.688 0.688 ...
..$ Pr( par2/par2 |y): num [1:9729] 0.312 0.312 0.312 0.312 0.312 ...
..- attr(*, "badpos")= int [1:13707] 25259 27250 27810 27880 27888 28836 30507 48975 55998 58734 ...
$ 4:'data.frame': 114 obs. of 23 variables:
..$ pos : int [1:114] 21119 21194 42177 64136 64146 74463 74465 74521 79860 79884 ...
..$ ref : chr [1:114] "T" "T" "C" "C" ...
..$ cons : chr [1:114] "C" "A" "Y" "Y" ...
..$ reads : chr [1:114] "cCCCCCCCCCCCCCcc" "aa" "T" "T" ...
..$ quals : chr [1:114] "IBFFBFBFFFFFFBBF" "FF" "F" "I" ...
..$ A : int [1:114] 0 2 0 0 0 0 0 0 2 0 ...
..$ C : int [1:114] 16 0 0 0 1 0 1 1 0 0 ...
..$ G : int [1:114] 0 0 0 0 0 0 0 0 0 2 ...
..$ T : int [1:114] 0 0 1 1 0 1 0 0 0 0 ...
..$ N : int [1:114] 0 0 0 0 0 0 0 0 0 0 ...
..$ bad : chr [1:114] NA NA NA NA ...
..$ par1ref : chr [1:114] "T" "T" "C" "C" ...
..$ par2ref : chr [1:114] "C" "A" "T" "T" ...
..$ read : Factor w/ 130 levels "1","2","3","4",..: 3 3 6 8 8 10 10 10 14 14 ...
..$ count : int [1:114] 16 2 1 1 1 1 1 1 2 2 ...
..$ read_allele : chr [1:114] "C" "A" "T" "T" ...
..$ Pr(y| par1/par1 ): num [1:114] 9.34e-12 4.99e-03 1.00e-02 1.00e-02 1.00e-02 ...
..$ Pr(y| par1/par2 ): num [1:114] 4.56e-10 2.33e-01 4.90e-01 4.90e-01 4.90e-01 ...
..$ Pr(y| par2/par2 ): num [1:114] 9.04e-10 8.61e-01 9.70e-01 9.70e-01 9.70e-01 ...
..$ est : int [1:114] 3 3 3 3 3 3 3 3 3 3 ...
..$ Pr( par1/par1 |y): num [1:114] 6.50e-24 4.49e-24 1.10e-26 2.53e-31 1.51e-31 ...
..$ Pr( par1/par2 |y): num [1:114] 1.56e-10 1.54e-10 5.77e-11 6.60e-12 6.59e-12 ...
..$ Pr( par2/par2 |y): num [1:114] 1 1 1 1 1 ...
..- attr(*, "badpos")= int [1:73] 16621 16638 34177 34180 74448 74464 78954 79664 80045 94170 ...
$ X:'data.frame': 2422 obs. of 23 variables:
..$ pos : int [1:2422] 34630 45427 70728 70744 166279 189892 207276 207424 213012 232229 ...
..$ ref : chr [1:2422] "T" "G" "G" "C" ...
..$ cons : chr [1:2422] "T" "G" "G" "C" ...
..$ reads : chr [1:2422] "a" "..." "^F." "." ...
..$ quals : chr [1:2422] "<" "IIF" "F" "B" ...
..$ A : int [1:2422] 1 0 0 0 0 0 0 4 0 1 ...
..$ C : int [1:2422] 0 0 0 1 1 0 2 0 0 0 ...
..$ G : int [1:2422] 0 3 1 0 0 1 0 1 1 0 ...
..$ T : int [1:2422] 0 0 0 0 0 0 0 0 0 0 ...
..$ N : int [1:2422] 0 0 0 0 0 0 0 0 0 0 ...
..$ bad : chr [1:2422] NA NA NA NA ...
..$ par1ref : chr [1:2422] "T" "G" "G" "C" ...
..$ par2ref : chr [1:2422] "A" "A" "A" "T" ...
..$ read : Factor w/ 2433 levels "1","2","3","4",..: 1 6 8 8 13 16 18 18 19 20 ...
..$ count : int [1:2422] 1 3 1 1 1 1 2 5 1 1 ...
..$ read_allele : chr [1:2422] "A" "G" "G" "C" ...
..$ Pr(y| par1/par1 ): num [1:2422] 0.0105 0.2732 0.9699 0.9696 0.9699 ...
..$ Pr(y| par1/par2 ): num [1:2422] 0.4895 0.0642 0.49 0.4899 0.49 ...
..$ Pr(y| par2/par2 ): num [1:2422] 0.96856 0.00134 0.01005 0.01012 0.01005 ...
..$ est : int [1:2422] 3 1 1 1 1 1 1 1 1 1 ...
..$ Pr( par1/par1 |y): num [1:2422] 1 1 1 1 1 ...
..$ Pr( par1/par2 |y): num [1:2422] 3.70e-08 2.00e-08 1.06e-08 1.06e-08 1.59e-09 ...
..$ Pr( par2/par2 |y): num [1:2422] 3.70e-18 9.35e-20 2.36e-23 2.23e-23 3.26e-26 ...
..- attr(*, "badpos")= int [1:2327] 34776 45619 86591 86607 166220 193151 193159 212997 232221 233552 ...