R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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> #exp.rawdata <- read.table("./copykat/data/GSM4476486_filtered_UMIcount_TNBC1.txt", header=T, sep='\t', check.names = F)
> exp.rawdata <- read.table("GSM4476486_filtered_UMIcount_TNBC1.txt", header=T, sep='\t', check.names = F)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'GSM4476486_filtered_UMIcount_TNBC1.txt': No such file or directory
> #exp.rawdata <- read.table("./copykat/data/GSM4476486_filtered_UMIcount_TNBC1.txt", header=T, sep='\t', check.names = F)
> exp.rawdata <- read.table("GSM4476486_filtered_UMIcount_TNBC1.txt", header=T, sep='\t', check.names = F)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'GSM4476486_filtered_UMIcount_TNBC1.txt': No such file or directory
> #exp.rawdata <-
read.table("./copykat/data/GSM4476486_filtered_UMIcount_TNBC1.txt", header=T, sep='\t', check.names = F)
> exp.rawdata <- read.table("GSM4476486_combined_UMIcount_CellTypes_TNBC1.txt", header=T, sep='\t', check.names = F)
> copykat.test <- copykat(rawmat=exp.rawdata,
+ id.type="S",
+ cell.line="no",
+ ngene.chr=5,
+ win.size=25,
+ KS.cut=0.15,
+ sam.name="TNBC1",
+ distance="euclidean",
+ n.cores=4)
Error in copykat(rawmat = exp.rawdata, id.type = "S", cell.line = "no", :
could not find function "copykat"
> install_github("navinlabcode/copykat")
Error in install_github("navinlabcode/copykat") :
could not find function "install_github"
> library(devtools)
載入需要的程輯包：usethis
Warning messages:
1: 程輯包‘devtools’是用R版本4.0.4 來建造的
2: 程輯包‘usethis’是用R版本4.0.3 來建造的
> install_github("navinlabcode/copykat")
Downloading GitHub repo navinlabcode/copykat@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: RcppArmad... (0.10.1.2.0 -> 0.10.4.0.0) [CRAN]
5: matrixStats (0.57.0 -> 0.58.0 ) [CRAN]
6: Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
7: MatrixModels (0.4-1 -> 0.5-0 ) [CRAN]
8: SparseM (1.78 -> 1.81 ) [CRAN]
9: quantreg (5.75 -> 5.85 ) [CRAN]
10: segmented (1.3-1 -> 1.3-3 ) [CRAN]
11: caTools (1.18.0 -> 1.18.2 ) [CRAN]
12: RcppParallel (5.0.2 -> 5.1.2 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:3
Installing 4 packages: mcmc, MCMCpack, dlm, parallelDist
Installing packages into ‘C:/Users/Nano/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/mcmc_0.9-7.zip'
Content type 'application/zip' length 1455359 bytes (1.4 MB)
downloaded 1.4 MB
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/MCMCpack_1.5-0.zip'
Content type 'application/zip' length 3653153 bytes (3.5 MB)
downloaded 3.5 MB
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/dlm_1.1-5.zip'
Content type 'application/zip' length 647932 bytes (632 KB)
downloaded 632 KB
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/parallelDist_0.2.4.zip'
Content type 'application/zip' length 1106778 bytes (1.1 MB)
downloaded 1.1 MB
package ‘mcmc’ successfully unpacked and MD5 sums checked
package ‘MCMCpack’ successfully unpacked and MD5 sums checked
package ‘dlm’ successfully unpacked and MD5 sums checked
package ‘parallelDist’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Nano\AppData\Local\Temp\RtmpKopzNf\downloaded_packages
√ checking for file 'C:\Users\Nano\AppData\Local\Temp\RtmpKopzNf\remotes2c0c7c1c4c6f\navinlabcode-copykat-0930c36/DESCRIPTION' ...
- preparing 'copykat':
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'copykat_1.0.4.tar.gz'
Installing package into ‘C:/Users/Nano/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'copykat' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'copykat'
finding HTML links ... 好了
CNA.MCMC html
annotateGenes.hg20 html
baseline.GMM html
baseline.norm.cl html
convert.all.bins.hg20 html
copykat html
exp.rawdata html
heatmap.3 html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (copykat)
> # library(devtools)
> #
> # install_github("navinlabcode/copykat")
> library('copykat')
載入程輯包：‘copykat’
The following object is masked _by_ ‘.GlobalEnv’:
exp.rawdata
> copykat.test <- copykat(rawmat=exp.rawdata,
+ id.type="S",
+ cell.line="no",
+ ngene.chr=5,
+ win.size=25,
+ KS.cut=0.15,
+ sam.name="TNBC1",
+ distance="euclidean",
+ n.cores=4)
[1] "running copykat v1.0.4"
[1] "step1: read and filter data ..."
[1] "33696 genes, 1097 cells in raw data"
[1] "12232 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
Error in parallel::mclapply(1:ncol(norm.mat), dlm.sm, mc.cores = n.cores) :
'mc.cores' > 1 is not supported on Windows
> copykat.test <- copykat(rawmat=exp.rawdata,
+ id.type="S",
+ cell.line="no",
+ ngene.chr=5,
+ win.size=25,
+ KS.cut=0.15,
+ sam.name="TNBC1",
+ distance="euclidean",
+ n.cores=1)
[1] "running copykat v1.0.4"
[1] "step1: read and filter data ..."
[1] "33696 genes, 1097 cells in raw data"
[1] "12232 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= 369
number of iterations= 1654
number of iterations= 206
WARNING! NOT CONVERGENT!
number of iterations= 5000
number of iterations= 826
number of iterations= 392
[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 26.08823 mins
