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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  tools parallel stats graphics grDevices utils datasets  methods base other attached packages:  flowQ_1.24.6 latticeExtra_0.6-26 RColorBrewer_1.0-5  parody_1.22.0 bioDist_1.36.0 KernSmooth_2.23-13  Biobase_2.24.0 mvoutlier_2.0.5 sgeostat_1.0-25  flowViz_1.28.22 flowCore_1.30.7 lattice_0.20-29  outliers_0.14 BiocGenerics_0.10.0 loaded via a namespace (and not attached):  annotate_1.42.1 AnnotationDbi_1.26.1 cluster_1.15.3  colorspace_1.2-4 compiler_3.1.2 corpcor_1.6.7  DBI_0.3.1 DEoptimR_1.0-2 digest_0.6.8  geneplotter_1.42.0 GenomeInfoDb_1.0.2 GGally_0.5.0  ggplot2_1.0.0 graph_1.42.0 grid_3.1.2  gtable_0.1.2 hexbin_1.27.0 IDPmisc_1.1.17  IRanges_1.22.10 MASS_7.3-35 munsell_0.4.2  mvtnorm_1.0-2 pcaPP_1.9-60 pls_2.4-3  plyr_1.8.1 proto_0.3-10 Rcpp_0.11.3  reshape_0.8.5 reshape2_1.4.1 robCompositions_1.9.0  robustbase_0.92-2 rrcov_1.3-8 RSQLite_1.0.0  scales_0.2.4 stats4_3.1.2 stringr_0.6.2  XML_3.98-1.1 xtable_1.7-4