Ben Heavner bheavner
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| example minid: ark:/57799/b9z705 | |
| TOMBSTONEd minid used in package: ark:/57799/b9j69h | |
| TOPMED parsed annotation chr 2 minid: minid:b9g69w |
bheavner
/ minids_from_R
Last active
June 15, 2018 18:51
Example of minting a minid with the minidtools R client
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| # goal: mint minids for freeze 5 annotation in exchange area. | |
| # requires digest and minidtools libraries | |
| # computes checksum using local copy of the file | |
| localPath <- | |
| paste0("/projects/topmed/variant_annotation/freeze_5/database/v0/", | |
| "parsed_files/2_snv.tsv.gz") | |
| # use location on exchange area for the location metadata in the minid |
bheavner
/ aggregate_ex.R
Created
August 6, 2017 21:50
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| library(tidyverse) | |
| parsed_snp_file <- "parsed_snp.tsv" | |
| parsed_indel_file <- "parsed_indel.tsv" | |
| unit_defs_file <- "feature_bounds_20170804.tsv" | |
| snps <- read_tsv(parsed_snp_file, comment = "#") | |
| indels <- read_tsv(parsed_indel_file, comment = "#") |
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| print("hello!") |
bheavner
/ test-testthat.R
Created
April 6, 2017 18:49
A simple test to ensure testthat is working (and to enable devtools::check() on an empty project)
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| context("test_testthat - unit tests") | |
| test_that("test_return_true returns TRUE", { | |
| expect_true(return_true()) | |
| }) |
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| return_true <- function(){ | |
| return(TRUE) | |
| } |
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| # don't commit files that may have passwords | |
| .env | |
| *.cnf | |
| # History files | |
| .Rhistory | |
| .Rapp.history | |
| # Session Data files | |
| .RData |
bheavner
/ gist:a8709acf26e02a6fb5015e20fab12837
Last active
March 29, 2016 23:22
library install checking for short course
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| print("Hi from github :)") | |
| print("Do you have randomForest?") | |
| # do we want specific versions? | |
| if(!require(randomForest, quiet = TRUE)){ | |
| install.packages("randomForest", quiet=TRUE) | |
| suppressWarnings(library(randomForest)) | |
| } |
bheavner
/ gist:a6c9bfe9d960542216d2
Created
November 11, 2015 00:34
Apply provenance to existing synapse object
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| metaDataOnly <- synGet(synapseId, downloadFile=F) | |
| activity_name <- "RNA-seq Count File Merging" | |
| input_files <- c("syn2875347") | |
| code_files <- list(list(name = "merge_mouse_tau_rnaseq_counts.R", | |
| url = "https://github.com/jaeddy/ampSynapseProjects/blob/v0.1-alpha/dataEnablement/R/merge_mouse_tau_rnaseq_counts.R", | |
| wasExecuted = T), | |
| list(name = "merge_count_files.R", | |
| url = "https://github.com/jaeddy/ampSynapseProjects/blob/v0.1-alpha/dataEnablement/R/merge_count_files.R", | |
| wasExecuted = T)) |