Error setting up a sample in OSAT
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Entering edit mode
@lluis-revilla-sancho
Last seen 1 day ago
European Union

I try to use the setup.sample that worked in the examples but I have found an error

library("OSAT")
pheno <- structure(list(`Sample Name_RNA` = c("001-w000", "001-w014"), 
IBD = c("CD", "CD")), row.names = 1:2, class = "data.frame")
gs <- setup.sample(pheno[1:2, c("Sample Name_RNA", "IBD")], optimal=c("Sample Name_RNA", "IBD"))
## Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column

In this case the data.frame is small, but it also fails with more rows

traceback()
## 11: stop(ngettext(sum(bad), "'by' must specify a uniquely valid column", 
##         "'by' must specify uniquely valid columns"), domain = NA)
## 10: fix.by(by.y, y)
## 9: merge.data.frame(tmp, cnt, by = s)
## 8: merge(tmp, cnt, by = s)
## 7: combineFactors(x, optimal, outNames = c("OrigRow", "oFactor"))
## 6: .local(.Object, ...)
## 5: initialize(value, ...)
## 4: initialize(value, ...)
## 3: new("gSample", x = x, optimal = optimal, strata = strata)
## 2: gSample(x, optimal, strata)
## 1: setup.sample(pheno[1:2, c("Sample Name_RNA", "IBD")], optimal = c("Sample Name_RNA", 
##        "IBD"))
devtools::session_info()
## Session info ------------------------------------------------------------------------------------------------
##  setting  value                       
##  version  R version 3.5.1 (2018-07-02)
##  system   i686, linux-gnu             
##  ui       RStudio (1.1.453)           
##  language en_US                       
##  collate  en_US.UTF-8                 
##  tz       Europe/Madrid               
##  date     2018-07-25                  
## 
## Packages ----------------------------------------------------------------------------------------------------
##  package    * version date       source        
##  backports    1.1.2   2017-12-13 CRAN (R 3.5.0)
##  base       * 3.5.1   2018-07-03 local         
##  compiler     3.5.1   2018-07-03 local         
##  crayon       1.3.4   2017-09-16 CRAN (R 3.5.0)
##  datasets   * 3.5.1   2018-07-03 local         
##  devtools   * 1.13.5  2018-02-18 CRAN (R 3.5.0)
##  digest       0.6.15  2018-01-28 CRAN (R 3.5.0)
##  evaluate     0.10.1  2017-06-24 CRAN (R 3.5.0)
##  graphics   * 3.5.1   2018-07-03 local         
##  grDevices  * 3.5.1   2018-07-03 local         
##  htmltools    0.3.6   2017-04-28 CRAN (R 3.5.0)
##  knitr        1.20    2018-02-20 CRAN (R 3.5.0)
##  magrittr     1.5     2014-11-22 CRAN (R 3.5.0)
##  memoise      1.1.0   2017-04-21 CRAN (R 3.5.0)
##  methods    * 3.5.1   2018-07-03 local         
##  OSAT       * 1.28.0  2018-07-24 Bioconductor  
##  pillar       1.3.0   2018-07-14 CRAN (R 3.5.0)
##  purrr        0.2.5   2018-05-29 CRAN (R 3.5.0)
##  Rcpp         0.12.17 2018-05-18 CRAN (R 3.5.0)
##  rlang        0.2.1   2018-05-30 CRAN (R 3.5.0)
##  rmarkdown    1.10    2018-06-11 CRAN (R 3.5.0)
##  rprojroot    1.3-2   2018-01-03 CRAN (R 3.5.0)
##  rsconnect    0.8.8   2018-03-09 CRAN (R 3.5.0)
##  rstudioapi   0.7     2017-09-07 CRAN (R 3.5.0)
##  stats      * 3.5.1   2018-07-03 local         
##  stringi      1.2.3   2018-06-12 CRAN (R 3.5.0)
##  stringr      1.3.1   2018-05-10 CRAN (R 3.5.0)
##  styler       1.0.1   2018-03-08 CRAN (R 3.5.0)
##  tibble       1.4.2   2018-01-22 CRAN (R 3.5.0)
##  tools        3.5.1   2018-07-03 local         
##  usethis    * 1.3.0   2018-02-24 CRAN (R 3.5.0)
##  utils      * 3.5.1   2018-07-03 local         
##  withr        2.1.2   2018-03-15 CRAN (R 3.5.0)
##  yaml         2.1.19  2018-05-01 CRAN (R 3.5.0)
osat • 674 views
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