Question: Rqc - envir must be either NULL, a list, or an environment.
1
gravatar for guus.steeg
2.7 years ago by
guus.steeg10
guus.steeg10 wrote:

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

software error bug library • 1.0k views
ADD COMMENTlink modified 2.7 years ago by Welliton Souza70 • written 2.7 years ago by guus.steeg10
Answer: Rqc - envir must be either NULL, a list, or an environment.
2
gravatar for Welliton Souza
2.7 years ago by
Brazil
Welliton Souza70 wrote:

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

 

ADD COMMENTlink written 2.7 years ago by Welliton Souza70

Thank you very much!

ADD REPLYlink written 2.7 years ago by guus.steeg10
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