Question: Programmatic use of flowQ?
0
gravatar for Kipper Fletez-Brant
4.6 years ago by
United States
Kipper Fletez-Brant150 wrote:

I am trying to understand flowQ and how to use it as a tool for flow data QA.  However, between the vignette and the reference manual, I cannot see a way to use method qa.timeline() as a way to easily and programmatically tell me which flow files in my data set have errors.  I see that I can do this using either the pictures produced by qa.timeline(), or the HTML interface, but I specifically want to be able to do something like asking which flow files do (or do not) have values above some threshold.

For completeness, the code I have tried, and session info:

> data(GvHD)
> dest <- tempdir()
> qp <- qaProcess.timeline(GvHD, channel="FL1-H", outdir=dest, cutoff=1)
creating summary plots....
creating frame plots......................................
There were 35 warnings (use warnings() to see them)
> qp
Quality process 'time line' of type 'time line'


> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] tools     parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] flowQ_1.24.6        latticeExtra_0.6-26 RColorBrewer_1.0-5 
 [4] parody_1.22.0       bioDist_1.36.0      KernSmooth_2.23-13 
 [7] Biobase_2.24.0      mvoutlier_2.0.5     sgeostat_1.0-25    
[10] flowViz_1.28.22     flowCore_1.30.7     lattice_0.20-29    
[13] outliers_0.14       BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] annotate_1.42.1       AnnotationDbi_1.26.1  cluster_1.15.3       
 [4] colorspace_1.2-4      compiler_3.1.2        corpcor_1.6.7        
 [7] DBI_0.3.1             DEoptimR_1.0-2        digest_0.6.8         
[10] geneplotter_1.42.0    GenomeInfoDb_1.0.2    GGally_0.5.0         
[13] ggplot2_1.0.0         graph_1.42.0          grid_3.1.2           
[16] gtable_0.1.2          hexbin_1.27.0         IDPmisc_1.1.17       
[19] IRanges_1.22.10       MASS_7.3-35           munsell_0.4.2        
[22] mvtnorm_1.0-2         pcaPP_1.9-60          pls_2.4-3            
[25] plyr_1.8.1            proto_0.3-10          Rcpp_0.11.3          
[28] reshape_0.8.5         reshape2_1.4.1        robCompositions_1.9.0
[31] robustbase_0.92-2     rrcov_1.3-8           RSQLite_1.0.0        
[34] scales_0.2.4          stats4_3.1.2          stringr_0.6.2        
[37] XML_3.98-1.1          xtable_1.7-4         

 

flowq flow cytometry • 662 views
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Kipper Fletez-Brant150
Answer: Programmatic use of flowQ?
1
gravatar for Kipper Fletez-Brant
4.6 years ago by
United States
Kipper Fletez-Brant150 wrote:

The correct answer, I discovered, is to (at the time of writing, at any rate) not use accessor methods, but instead directly get at slots in the resulting qaProcess object.  

Using the 'qp' object from above, I can ask for each file ('frameProcess') whether it passed or no, as well as the value of the test:

> qp@frameProcesses[[1]]@summaryAggregator@passed
[1] TRUE
> qp@frameProcesses[[1]]@summaryAggregator@x
[1] 1
Levels: 1
ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Kipper Fletez-Brant150
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