NCBI-Hackathons/HLAClustRView
HLA typing clustering and visualization based on specific similarity metrics

Package index
Search the NCBI-Hackathons/HLAClustRView package
Vignettes
Functions
52
Source code
20
Man pages
28
Home
/
GitHub
/
NCBI-Hackathons/HLAClustRView
/
tests/testthat/test-parseHLADataset.R

tests/testthat/test-parseHLADataset.R
In NCBI-Hackathons/HLAClustRView: HLA typing clustering and visualization based on specific similarity metrics 

### Unit tests for functions in parseHLADataset.R file

library(HLAClustRView)



directory <- system.file("extdata", package = "HLAClustRView")
fileName <- paste0(directory, "/Samples_HLA_typing.txt")


### Tests readHLADataset() function

context("Test for readHLADataset() function")

test_that("readHLADataset() must return an error when hlaFilePath is a number", {
    message <- "The hlaFilePath parameter must by a character string"
    expect_error(readHLADataset(hlaFilePath = 33), message)
})

test_that("readHLADataset() must return an error when hlaFilePath is a number", {
    message <- "The hlaFilePath parameter must by a character string"
    expect_error(readHLADataset(hlaFilePath = TRUE), message)
})

test_that("parseHLADbAlignment() must return an error when hlaFilePath does not exist", {
    path_to_test <- "./3_21_33eddger_39kdf_23sk2-2221fvd_qqqqqqqqqq_2.txt"
    if (!dir.exists(path_to_test)) {
        message <- paste0("The file '", path_to_test, "' must be a valid text file")
        expect_error(readHLADataset(hlaFilePath = path_to_test), message)
    }
})

test_that("parseHLADbAlignment() must return good result", {
    result <- readHLADataset(hlaFilePath = fileName)

    expected <- list()

    SampleName <- c("ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053",
                    "ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053",
                    "ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053",
                    "ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053",
                    "ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053","ERR188053",
                    "ERR188053","ERR188053","ERR188053","ERR188465","ERR188465","ERR188465","ERR188465",
                    "ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465",
                    "ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465",
                    "ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465",
                    "ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465",
                    "ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188465","ERR188040",
                    "ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040",
                    "ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040",
                    "ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040",
                    "ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040",
                    "ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040","ERR188040",
                    "ERR188040","ERR188040","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189",
                    "ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189",
                    "ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189",
                    "ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189",
                    "ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188189",
                    "ERR188189","ERR188189","ERR188189","ERR188189","ERR188189","ERR188117","ERR188117",
                    "ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117",
                    "ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117",
                    "ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117",
                    "ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117",
                    "ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117","ERR188117")

    AlleleName <- c("1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1",
                    "2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2",
                    "1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1",
                    "2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2",
                    "1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1",
                    "2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2",
                    "1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1",
                    "2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2",
                    "1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2","1","2")

    GeneName <- c("A","A","B","B","C","C","DMA","DMA","DMB","DMB","DOA","DOA","DOB","DOB","DPA1","DPA1","DPB1","DPB1",
                  "DQA1","DQA1","DQB1","DQB1","DRA","DRA","DRB1","DRB1","E","E","F","F","MICA","MICA","MICB","MICB","TAP1",
                  "TAP1","TAP2","TAP2","A","A","B","B","C","C","DMA","DMA","DMB","DMB","DOA","DOA","DOB","DOB","DPA1","DPA1",
                  "DPB1","DPB1","DQA1","DQA1","DQB1","DQB1","DRA","DRA","DRB1","DRB1","E","E","F","F","MICA","MICA","MICB",
                  "MICB","TAP1","TAP1","TAP2","TAP2","A","A","B","B","C","C","DMA","DMA","DMB","DMB","DOA","DOA","DOB","DOB",
                  "DPA1","DPA1","DPB1","DPB1","DQA1","DQA1","DQB1","DQB1","DRA","DRA","DRB1","DRB1","E","E","F","F","MICA",
                  "MICA","MICB","MICB","TAP1","TAP1","TAP2","TAP2","A","A","B","B","C","C","DMA","DMA","DMB","DMB","DOA",
                  "DOA","DOB","DOB","DPA1","DPA1","DPB1","DPB1","DQA1","DQA1","DQB1","DQB1","DRA","DRA","DRB1","DRB1","E",
                  "E","F","F","MICA","MICA","MICB","MICB","TAP1","TAP1","TAP2","TAP2","A","A","B","B","C","C","DMA","DMA",
                  "DMB","DMB","DOA","DOA","DOB","DOB","DPA1","DPA1","DPB1","DPB1","DQA1","DQA1","DQB1","DQB1","DRA","DRA",
                  "DRB1","DRB1","E","E","F","F","MICA","MICA","MICB","MICB","TAP1","TAP1","TAP2","TAP2")

    AlleleGroup <- c("31","68","27","27","02","02","01","01","01","01","01","01","01","01","01","01","04","04","01","03","03",
                     "06","01","01","13","04","01","01","01","01","007","045","010","010","01","01","02","01","24","02","51",
                     "14","14","08","01","01","01","01","01","01","01","01","01","01","03","02","04","05","04","03","01","01",
                     "13","08","01","01","01","01","011","049","005","010","02","04","02","01","29","01","44","08","07","16",
                     "01","01","01","01","01","01","01","01","01","02","01","02","02","05","02","02","01","01","03","07","01",
                     "01","01","01","008","004","010","010","01","01","01","01","32","02","53","44","04","05","01","01","01",
                     "01","01","01","01","01","01","01","104","04","03","01","03","06","01","01","04","13","01","01","01","01",
                     "002","008","010","010","01","01","02","01","03","25","07","18","07","12","01","01","01","01","01","01",
                     "01","01","01","01","04","04","01","01","06","06","01","01","15","15","01","01","01","01","008","018","028","002","01","02","01","01")

    Protein <- c("01","01","05","05","02","02","01","02","03","01","01","01","01","01","03","03","01","01","03","03","02","03",
                 "01","02","01","01","01","03","01","01","01",NA,NA,NA,"01","01","01","01","02","01","01","02","02","02",
                 "02","01","03","01","01","01","01","04","03","03","01","01","01","05","02","01","02","02","03","01","03","01",
                 "01","01",NA,NA,"03",NA,"01","01","01","02","02","01","03","01","01","01","01","01","03","01","01","01",
                 "01","01","03","01","01","01","01","01","01","02","01","02","01","01","01","03","01","01","01",NA,NA,NA,
                 "01","01","01","01","01","01","01","02","09","01","01","01","03","03","01","01","01","01","03","03","01","01",
                 "01","02","02","04","01","02","04","02","03","01","01","01","01","01",NA,NA,"01","01","01","02","01","01",
                 "02","01","02","03","01","01","01","01","01","01","01","01","03","03","01","01","02","02","02","02","02","02",
                 "01","01","01","03","03","01","04","01",NA,"01","01","01","01","02")

    SynSubst <- c("02","01","02","02","02","02","01",NA,"01","01","04","02","03","01","01","01","01","01","01","01","01","01","01",
                  "02","01","01","01","02","01","01",NA,NA,NA,NA,"01","01","02","03","01","01","01","01","01","01",NA,"01",
                  "01","01","06","01","01","01","01","01","01","02","01","01","01","01","02","02","01","01","02","01","01","02",NA,
                  NA,NA,NA,"01",NA,"02",NA,"01","01","01","01","01","01","01","01","01","01","02","02","01","03","01","02",
                  "01","02","01","01","01","01","01","02","01","01","01","02","01","01","01",NA,NA,NA,"01","01","03","03","01",
                  "01","01","01",NA,"01","01","01","01","01","02","02","01","01","01","01",NA,"01","01","01","01","01","01","02",
                  "01","01","02","01","01","01",NA,"01",NA,NA,"01","01","02",NA,"01","01","01","01","01","01","01","01","01",
                  "01","02","01","01","03","01","01","01","01","01","01","01","01","03","03","01","01","01","02","01","01",NA,NA,NA,"01","01","01","03",NA)

    NonCoding <- c("01","01",NA,NA,"01","01","01",NA,"01","01","02","01","01","01","01","01","01","01","01","01",NA,NA,"01",NA,
                   "01",NA,"01","01","01","01",NA,NA,NA,NA,"01","01","01","01","01","01","01","01","01","01",NA,"01","01","01",
                   NA,NA,"01","01","01","01",NA,NA,NA,"01",NA,"01",NA,NA,NA,NA,"01","01","01","01",NA,NA,NA,NA,
                   NA,NA,"01",NA,"01","01","01",NA,"01","01","01","01","01","01","01","01","01","01","01",NA,NA,NA,"01","01",
                   NA,"01","01",NA,"01","01","01","01","01","01",NA,NA,NA,NA,"01","01","01","01",NA,"01",NA,"01",NA,"01",
                   "01","01","01","01","01","01","01","01","01","01",NA,"01",NA,"01",NA,NA,"01",NA,NA,NA,"01","01","01","01",
                   NA,NA,NA,NA,"01","01","01",NA,"01",NA,NA,"01","01","01","01","01","01","01","01",NA,"01","01","01","01",
                   "01","01","01","01",NA,NA,NA,NA,"01","01","01","01","01","01",NA,NA,NA,NA,"01",NA,"01",NA)

    Suffix <- c(NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
                 NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
                 NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
                 "novel",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
                 NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,"N",NA,NA,NA,NA,NA,
                 NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,"updated",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,"novel",
                 "novel",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,
                 NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA)


    expected[["data"]] <- tibble(SampleName=SampleName, AlleleName=AlleleName, GeneName=GeneName,
                                 AlleleGroup=AlleleGroup, Protein=Protein,
                                 SynSubst=SynSubst, NonCoding=NonCoding, Suffix=Suffix)

    class(expected) <- "HLADataset"

    expect_equal(result, expected)

})
NCBI-Hackathons/HLAClustRView documentation built on Nov. 22, 2019, 6:11 a.m.

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close