R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

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> knitr::opts_chunk$set(
+   collapse = TRUE,
+   comment = "#>"
+ )
> copykat.test <- copykat(rawmat=exp.rawdata, sam.name="test")
Error in copykat(rawmat = exp.rawdata, sam.name = "test") : 
  could not find function "copykat"
> # library(devtools)
> # install_github("navinlabcode/copykat")
> library(copykat)
> copykat.test <- copykat(rawmat=exp.rawdata, sam.name="test")
[1] "running copykat v1.0.4"
[1] "step1: read and filter data ..."
[1] "33694 genes, 302 cells in raw data"
[1] "12156 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
[1] "step 4: measuring baselines ..."
number of iterations= 315 
number of iterations= 679 
number of iterations= 214 
number of iterations= 823 
number of iterations= 431 
number of iterations= 823 
[1] "step 5: segmentation..."
[1] "step 6: convert to genomic bins..."
[1] "step 7: adjust baseline ..."
[1] "step 8: final prediction ..."
[1] "step 9: saving results..."
[1] "step 10: ploting heatmap ..."

Time difference of 5.843387 mins

image.png

运行2

> # library(devtools)
> # install_github("navinlabcode/copykat")
> library(copykat)
> dim(exp.rawdata)
[1] 33694   302
> copykat.test <- copykat(rawmat=exp.rawdata, 
+                         ngene.chr = 25,
+ sam.name="test")
[1] "running copykat v1.0.4"
[1] "step1: read and filter data ..."
[1] "33694 genes, 302 cells in raw data"
[1] "12156 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
[1] "step 4: measuring baselines ..."
number of iterations= 331 
number of iterations= 346 
number of iterations= 793 
number of iterations= 864 
number of iterations= 742 
number of iterations= 823 
[1] "step 5: segmentation..."
[1] "step 6: convert to genomic bins..."
[1] "step 7: adjust baseline ..."
[1] "step 8: final prediction ..."
[1] "step 9: saving results..."
[1] "step 10: ploting heatmap ..."
Time difference of 3.815094 mins
> pred.test <- data.frame(copykat.test$prediction)
> CNA.test <- data.frame(copykat.test$CNAmat)
> dim(pred.test)
[1] 257   2
> dim(CNA.test)
[1] 12167   260

运行3 同1

> library(copykat)
> dim(exp.rawdata)
[1] 33694   302
> copykat.test <- copykat(rawmat=exp.rawdata, 
+                         ngene.chr = 0,
+ sam.name="test")
[1] "running copykat v1.0.4"
[1] "step1: read and filter data ..."
[1] "33694 genes, 302 cells in raw data"
[1] "12156 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
[1] "step 4: measuring baselines ..."
number of iterations= 315 
number of iterations= 679 
number of iterations= 214 
number of iterations= 823 
number of iterations= 431 
number of iterations= 823 
[1] "step 5: segmentation..."
[1] "step 6: convert to genomic bins..."
[1] "step 7: adjust baseline ..."
[1] "step 8: final prediction ..."
[1] "step 9: saving results..."
[1] "step 10: ploting heatmap ..."
Time difference of 3.96542 mins
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