-includes additional options:
--ref_subtract_method=REFERENCE_SUBTRACTION_METHOD
Method used to subtract the reference values from the observations. Valid choices are: by_mean, by_quantiles [Default by_mean]
--hclust_method=HIERARCHICAL_CLUSTERING_METHOD
Method used for hierarchical clustering of cells. Valid choices are: ward.D, ward.D2, single, complete, average, mcquitty, median, centroid [Default complete]
The --steps parameter now generates a full inferCNV heatmap/plot for each of the data transformation operations performed.
The log transformation log2(x/10 + 1) to generate transcripts(or counts) per 100k instead of per million is now more simply log2(x+1). If the user wants to study counts-per-100k or counts-per-10k, that is entirely fine... The log transformation will simply be log2(whatever + 1).
-sample data is updated using a random selection of 400 malignant oligodendroglioma cells and ~100 normal cells, described in file '__sampled_cells.annotations.dat'. The actual gene names and cell names are provided instead of the generic gene_ and cell_ values. Data is from Tirosh et al. Nature 2016.
