Mercurial > repos > fwuennemann > alevinqc
comparison alevinQC_galaxy/run_alevinQC.R @ 0:5f0da20666fa draft default tip
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| author | fwuennemann |
|---|---|
| date | Thu, 01 Apr 2021 00:55:48 +0000 |
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| -1:000000000000 | 0:5f0da20666fa |
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| 1 ## Run alevinQC inside of Galaxy | |
| 2 | |
| 3 ## Check that input files are formatted correctly | |
| 4 library(alevinQC) | |
| 5 | |
| 6 ## Check that all input files required are present in working directory | |
| 7 checkAlevinInputFiles(baseDir = ".") | |
| 8 | |
| 9 ## Read in alevin output files as alevin object | |
| 10 alevin <- readAlevinQC(baseDir = ".") | |
| 11 | |
| 12 # ## Write table with statistics of run | |
| 13 summaryTable <- alevin$summaryTables$fullDataset | |
| 14 | |
| 15 write.table(summaryTable, | |
| 16 file ="./summaryTable.tab", | |
| 17 sep = "\t", | |
| 18 col.names = FALSE, | |
| 19 row.names = TRUE, | |
| 20 quote = FALSE) | |
| 21 | |
| 22 ## Plot knee plot | |
| 23 pdf(file = "./alevin_kneeplot.pdf") | |
| 24 plotAlevinKneeRaw(alevin$cbTable) | |
| 25 dev.off() | |
| 26 | |
| 27 ## Barcode collapse plot | |
| 28 pdf(file = "./alevin_barodeFrequency_quant.pdf", width = 12, height = 9) | |
| 29 plotAlevinQuant(alevin$cbTable) | |
| 30 dev.off() |