19995: Skip GLM on variants below frequency threshold.

[lightning.git] / slicenumpy.go

diff --git a/slicenumpy.go b/slicenumpy.go
index 895c3c15fa2d91cfd7b153f65d6b78a9c59ad806..c3d02a99bc91a9bfa98093c9d95b1f2568361268 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -44,6 +44,7 @@ type sliceNumpy struct {
        threads         int
        chi2Cases       []bool
        chi2PValue      float64
+       glmMinFrequency float64
        pcaComponents   int
        minCoverage     int
        includeVariant1 bool
@@ -94,6 +95,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
        debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
        flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
        flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test (or logistic regression if -samples file has PCA components) and omit columns with p-value above this threshold")
+       flags.Float64Var(&cmd.glmMinFrequency, "glm-min-frequency", 0.01, "skip GLM calculation on tile variants below this frequency in the training set")
        flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
        cmd.filter.Flags(flags)
        err := flags.Parse(args)
@@ -151,6 +153,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        "-pca-components=" + fmt.Sprintf("%d", cmd.pcaComponents),
                        "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
                        "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
+                       "-glm-min-frequency=" + fmt.Sprintf("%f", cmd.glmMinFrequency),
                        "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
                        "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
                }
@@ -302,7 +305,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
        }
 
        if len(cmd.samples[0].pcaComponents) > 0 {
-               cmd.pvalue = glmPvalueFunc(cmd.samples, cmd.pcaComponents)
+               cmd.pvalue = glmPvalueFunc(cmd.samples, cmd.pcaComponents, cmd.glmMinFrequency)
                // Unfortunately, statsmodel/glm lib logs stuff to
                // os.Stdout when it panics on an unsolvable
                // problem. We recover() from the panic in glm.go, but