illumina / happycompare Goto Github PK
View Code? Open in Web Editor NEWReporting toolbox for happy output
Home Page: https://illumina.github.io/happyCompare
License: Other
Reporting toolbox for happy output
Home Page: https://illumina.github.io/happyCompare
License: Other
Hi,
The 'vignettes/pcrfree_vs_nano.subset.csv' given in quickstart guide example seems to be missing from package. When I load happyCompare library, I encounter the following error.
Commands:
devtools::install_github("Illumina/happyCompare")
library(happyCompare)
samplesheet_path <- "vignettes/pcrfree_vs_nano.subset.csv"
happy_compare <- read_samplesheet(samplesheet_path, lazy = TRUE)
Error:
Reading happyCompare samplesheet
Error in read_samplesheet(samplesheet_path, lazy = TRUE) :
Cannot find samplesheet: vignettes/pcrfree_vs_nano.subset.csv
When I try to search for for any cv file in happyCompare package, I find pcrfree_vs_nano.tests.csv. However, providing that path to read_samplesheet also gives an error.
Command:
samplesheet_path <- system.file('tests','testthat','pcrfree_vs_nano.tests.csv', package='happyCompare')
happy_compare <- read_samplesheet(samplesheet_path, lazy = TRUE)
Error:
Reading happyCompare samplesheet
Parsed with column specification:
cols(
Group.Id = col_character(),
Sample.Id = col_character(),
Replicate.Id = col_character(),
happy_prefix = col_character(),
build_metrics = col_character()
)
Processing ../data/pcrfree_vs_nano/filtered_happy/NA12878-I30_S1
Error in check_happy_path(happy_prefix) :
Can't read directory: ../data/pcrfree_vs_nano/filtered_happy
Command: find /Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare/ -name "*.csv" -print
Output:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/build_metrics/NA12878-I30_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/build_metrics/NA12878-I33_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/build_metrics/NA12878-R1_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/build_metrics/NA12878-R2_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I30_S1.extended.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I30_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I33_S1.extended.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-I33_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.extended.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R1_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.extended.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/data/pcrfree_vs_nano/filtered_happy/NA12878-R2_S1.summary.csv
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/happyCompare//tests/testthat/pcrfree_vs_nano.tests.csv
Thanks,
Shruti
Shruti Marwaha, PhD.
Research Engineer,
Stanford Center for Undiagnosed Diseases
Stanford University
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.