I've downloaded an example FASTQ file from: http://www.internationalgenome.org/data-portal/sample/HG00119

file: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR043/SRR043348/SRR043348_1.fastq.gz

Subsetted the data to only keep first 100,000 reads (400,000 lines). Continue according to page: https://bioconductor.org/packages/release/bioc/vignettes/Rqc/inst/doc/Rqc.html

I load in the file: `rqcResultSet <- rqc("./Data", "SRR043348_1_100000.fastq", openBrowser = F)`

and run: `rqcShinyReport(rqcResultSet)`

I get the following error:

Warning: Error in eval.quoted: envir must be either NULL, a list, or an environment.
Stack trace (innermost first):
    107: eval.quoted
    106: splitter_d
    105: ddply
    104: rqcReadQualityCalc
    103: plots[[input$plot]]
    102: renderPlot
     92: <reactive:plotObj>
     81: plotObj
     80: origRenderFunc
     79: output$rqcPlotExample
      2: runApp
      1: rqcShinyReport

Since splitter_d is part of the "plyr" package, what can I do if I can't access the functions? According to google something needs to be converted to a data.frame, but everything already is. Do I miss something that is essential for this analysis?

Regards,

Guus

Hi guus.steeg, thank you for posting this issue.

I am the developer of Rqc package. The rqc and rqcQA functions should return a list of RqcResultSet objects. When you pass only one input file these functions return the object itself, which make the other functions fail (my fault). A workaround for this bug is to add the object into a list. Using your example:

library(Rqc)
rqcResultSet <- rqcQA("SRR043348_1.fastq.gz", sample=100000)
rqcResultSet <- list(SRR043348_1 = rqcResultSet)
rqcShinyReport(rqcResultSet)

I will fix this bug soon as possible.

Remember to add the package name as tag. It helps us to find and answer the questions quicker.

Best regards,

Welliton