|
0
|
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() |
