Difference between revisions of "HLab:Rscripts"
From CCGB
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Heatmaps | Heatmaps | ||
| + | *Kmeans clustering and heatmap for differential expression. This script takes inputs of input table, outfile, column names, and k. The input table is expected to have rownames (genes). The column name input is comma separated text. The output includes the pdf named using outfile and geneClusters.txt. | ||
| + | ** [[Media:kmeans.r.txt|kmeans.r]] | ||
GEDI | GEDI | ||
Return to [[HLab:Main|main]] | Return to [[HLab:Main|main]] | ||
Revision as of 16:26, 19 December 2014
Miscellaneous R Scripts
Quantile normalization
- This can be used directly or as an example. It takes an input and output file names (tab-delimited files with header and row names). It is set up for RNA and adds 1.1 to the expression levels to avoid zeros before taking the log2(normalized expr). normalize.r
Scatter plots for replicates
- This is an example. File names and number of columns are hard coded and will need changed to match your usage. The first one plots the points all the same color. For graphs that are very dense the second one changes the colors depending on the number of bins in the vicinity of the one being plotted (red is dense).
PCA
Heatmaps
- Kmeans clustering and heatmap for differential expression. This script takes inputs of input table, outfile, column names, and k. The input table is expected to have rownames (genes). The column name input is comma separated text. The output includes the pdf named using outfile and geneClusters.txt.
GEDI
Return to main
