Table 1 Main functions for a differential gene presence/absence analysis with deltaRpkm. Functions are listed in the chronological order of usage
Function name | Description | Output(s) |
|---|---|---|
loadMetadata() | format the user metadata table | data frame of the design table |
rpkm() | convert read counts to RPKM | data frame of RPKM values |
deltarpkm() | compute pairwise δRPKM values (samples from group 1 ~ samples from group 2) | data frame of samples inter-group δRPKM values, per gene |
deltaRPKMStats() | compute 1) median δRPKM values of each gene, 2) global standard deviation of all medians and 3) selection of genes passing a given threshold | data frame with genes annotated as differentially present in reference group 1 versus comparison group 2 |
median_plot() | diagnostics plot to visualize the median δRPKM values of each gene and highlight the selected genes dsitribution | deltaRpkm_medians_plot.pdf file in the working directory |
rpkmHeatmap() | heatmap of the RPKM values of the selected set of genes | deltaRpkm_heatmap.tiff file in the working directory |