Entering edit mode
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)
