getDiffExpressedGenes {RTCGAToolbox} | R Documentation |
getDiffExpressedGenes
returns a list that stores the results for each dataset.
getDiffExpressedGenes( dataObject, DrawPlots = TRUE, adj.method = "BH", adj.pval = 0.05, raw.pval = 0.05, logFC = 2, hmTopUpN = 100, hmTopDownN = 100, meanFilter = 10 )
dataObject |
This must be |
DrawPlots |
A logical parameter to draw heatmaps and volcano plots. |
adj.method |
Raw p value adjustment methods (Default "BH") |
adj.pval |
Adjusted p value cut off for results table (Default 0.05) |
raw.pval |
raw p value cut off for results table (Default 0.05) |
logFC |
log fold change cut off for results table (Default 2) |
hmTopUpN |
Max number of up regulated genes in heatmap (Default 100) |
hmTopDownN |
Max number of down regulated genes in heatmap (Default 100) |
meanFilter |
Mean read counts for each gene to filter not expressed genes (Default 10) |
Returns a list that stores results for each dataset
data(accmini)