CHECK report for ISoLDE on veracruz1
This page was generated on 2018-04-12 13:42:34 -0400 (Thu, 12 Apr 2018).
ISoLDE 1.6.0 Christelle Reynès
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/ISoLDE |
Branch: RELEASE_3_6 |
Last Commit: d722d6f |
Last Changed Date: 2017-10-30 12:41:14 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
Summary
Command output
Installation output
ISoLDE.Rcheck/00install.out
Tests output
ISoLDE.Rcheck/tests/testsIsolde.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(ISoLDE)
>
> targetfile <- system.file("extdata", "target_file.txt", package = "ISoLDE")
> rawfile <- system.file("extdata", "rawASRcounts_file.txt", package = "ISoLDE")
> normfile <- system.file("extdata", "normASRcounts_file.txt", package = "ISoLDE")
>
> rawASRcounts <- readRawInput(raw_file = rawfile, del = "tab", rownames = TRUE, colnames = TRUE)
Reading raw input file...
Done
> normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
Reading normalized input file...
Done
> target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
Reading target file...
Done
>
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
Filtering your data...
Filtering threshold is 3
Done
> filteredASRcounts <- res_filterT$filteredASRcounts
> resiso<-isolde_test(bias = "parental", asr_counts = filteredASRcounts, target = target, graph = TRUE, text = FALSE, ext = "png", nboot = 3000,pcore=1)
Warning: pcore is a percentage between 0 and 100, be sure you want to use 1% of your available cores.
ISoLDE is searching for allele-specific gene expression due to parental biases...
Done
According to the satisfying number of replicates the full method can be applied. See the vignette for more details
Testing...
This step can last for a few minutes. Please be patient :)
Note: the full method uses a bootstrap step which means some results might change from one test to another.
Open MP enabled
Have Cores : 8
UseCores : 1
nu0= 0.200000
Open MP enabled
Have Cores : 8
UseCores : 1
lambda0 : 1.600000
Open MP enabled
Have Cores : 8
UseCores : 1
nu0= 0.100000
Open MP enabled
Have Cores : 8
UseCores : 1
lambda0 : 1.500000
Open MP enabled
Have Cores : 8
UseCores : 1
nu0= 0.200000
Open MP enabled
Have Cores : 8
UseCores : 1
lambda0 : 1.600000
Done
52 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_04-12-2018_05-26-39.tsv.
6068 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-12-2018_05-26-39.tsv.
57 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-12-2018_05-26-39.tsv.
Among these undetermined (UN) genes, 24 genes are coherent.
These genes correspond to the ones with the flag column set on "FLAG_consistency" of "FLAG_significance" in the undetermined genes file. See the vignette for more information on flags.
0 genes have been filtered due to few reads.
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="strain")
Filtering your data...
Filtering threshold is 3
Done
> filteredASRcounts <- res_filterT$filteredASRcounts
> resiso<-isolde_test(bias = "strain", asr_counts = filteredASRcounts, target = target, graph = TRUE, text = FALSE, ext = "png", nboot = 3000, method = "threshold")
ISoLDE is searching for allele-specific gene expression due to strain biases...
The predefined threshold method is about to proceed, but we strongly recommand the bootstrap method because ISoLDE detected more than 2 replicates in each cross.
Testing...
Done
308 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_04-12-2018_05-26-41.tsv.
4622 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-12-2018_05-26-41.tsv.
1330 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-12-2018_05-26-41.tsv.
Among these undetermined (UN) genes, 913 genes are coherent.
These genes correspond to the ones with the flag column set on "FLAG_consistency" of "FLAG_significance" in the undetermined genes file. See the vignette for more information on flags.
0 genes have been filtered due to few reads.
>
> proc.time()
user system elapsed
66.852 0.856 68.790
Example timings
ISoLDE.Rcheck/ISoLDE-Ex.timings