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Roleren / ORFik

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Error in validateExperiments(df): stage and libtype must be colnames in df! #157

Closed SuhasSrinivasan closed 5 months ago

SuhasSrinivasan commented 5 months ago

Hi,

Thank you for making this helpful package and hope this can be a unifying tool!

I am currently following the Ribo-seq vignette to load some Ribo-seq data https://bioconductor.org/packages/release/bioc/vignettes/ORFik/inst/doc/Ribo-seq_pipeline.html

However, there is an issue at this step list.experiments() 

Error: BiocParallel errors
  2 remote errors, element index: 1, 2
  0 unevaluated and other errors
  first remote error:
Error in validateExperiments(df): stage and libtype must be colnames in df!

I am not sure about the BiocParallel error, but traced the validateExperiment to here: https://github.com/Roleren/ORFik/blob/49a3d30beb8e9d2bfd8df1db4ee9d4b6b9cf42cc/R/experiment.R#L88

Help would be greatly appreciated!

SuhasSrinivasan commented 5 months ago

Following the vignette, create.experiment() was not supplied with libtype and stage, i.e., default auto.

After supplying values, e.g., libtype = RFP and stage = CellLine verified that the CSV file written to directory ORFik_experiments contains the changes.

However, the error still persists.

SuhasSrinivasan commented 5 months ago

Copying the CSV file so that it can be helpful.

create.experiment(file.path(config_inf['bam Ribo-seq'], 'aligned/'),
                  exper = config_inf['exp Ribo-seq'],
                  fa = annotation['genome'],
                  txdb = paste0(annotation['gtf'], '.db'),
                  organism = organism,
                  pairedEndBam = T,
                  libtype = 'RFP',
                  stage = 'CellLine',
                  condition = rep(c('CHX', 'LTM'), each = 4))

colo_riboseq_Ribo-seq.csv

Roleren commented 5 months ago

This error was related to pairedEndBam flag and is now fixed in #159