inst/unitTests/test_ExcelProteomicsImporter.R
In paul-shannon/ExcelProteomicsImporter: ExcelProteomicsImporter
# test_ExcelProteomicsImporter.R
#------------------------------------------------------------------------------------------------------------------------
Sys.setlocale("LC_ALL", "C")
#------------------------------------------------------------------------------------------------------------------------
library(ExcelProteomicsImporter)
library(RUnit)
library(yaml)
#------------------------------------------------------------------------------------------------------------------------
test.files <- file.path(system.file(package="ExcelProteomicsImporter", "extdata"),
c("test_data2_LCL57cell_line_experiment2.txt",
"test_data3_PBMC_experiment.txt",
"test_data4_Glioma_cell_line_experiment.txt",
"test_data_LCL57cell_line_experiment_clean.txt"))
#------------------------------------------------------------------------------------------------------------------------
runTests <- function()
{
test_ctor()
test_validateColumnNames()
test_groupCount()
test_groupBoundaries_file1()
test_groupBoundaries_file2()
test_groupBoundaries_file3()
test_groupBoundaries_file4()
test_getConditionFilenames()
test_toYAMLreadyList_file1()
test_toYAMLreadyList_file2()
test_toYAMLreadyList_file3()
test_toYAMLreadyList_file4()
test_toYAML_file1()
test_toYAML_file2()
test_toYAML_file3()
test_toYAML_file4()
} # runTests
#------------------------------------------------------------------------------------------------------------------------
test_ctor <- function()
{
message(sprintf("--- test_ctor"))
for(file in test.files){
checkTrue(file.exists(file))
importer <- ExcelProteomicsImporter(file)
tbl.raw <- getRawTable(importer)
checkTrue(nrow(tbl.raw) %in% c(39, 37, 33, 37))
checkTrue(ncol(tbl.raw) %in% c(15, 37, 29, 25))
}
} # test_ctor
#------------------------------------------------------------------------------------------------------------------------
test_validateColumnNames <- function()
{
message(sprintf("--- test_validateColumnNames"))
for(file in test.files){
#printf("--- %s", file)
importer <- ExcelProteomicsImporter(file)
checkTrue(validateColumnNames(importer))
}
} # test_validateColumnNames
#------------------------------------------------------------------------------------------------------------------------
test_groupCount <- function()
{
message(sprintf("--- test_groupCount"))
# first file has just one group, so just one "avg" colname, one "stdev"
x <- ExcelProteomicsImporter(test.files[1])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
# second file has just one group, so just one "avg" colname, one "stdev"
x <- ExcelProteomicsImporter(test.files[2])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
# third file has just one group, so just one "avg" colname, one "stdev"
x <- ExcelProteomicsImporter(test.files[3])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
# fourth file has two groups, so two "avg" colnames, two "stdev"
x <- ExcelProteomicsImporter(test.files[4])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
} # test_groupCount
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file1 <- function()
{
message(sprintf("--- test_groupBoundaries_file1"))
expected.cols <- c("LCL57_IR_00Gy_1", "LCL57_IR_01Gy_1", "LCL57_IR_02Gy_1", "LCL57_IR_05Gy_1", "LCL57_IR_10Gy_1")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[1])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(39, 15))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 5)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 5)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file1
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file2 <- function()
{
message(sprintf("--- test_groupBoundaries_file2"))
expected.cols <- c("PBMC+SEB_DMSO_0Gy_1", "PBMC+SEB_DMSO_5Gy_1", "PBMC+SEB_ATMi_0Gy_1",
"PBMC+SEB_ATMi_5Gy_1", "PBMC+SEB_DNAPKi_0Gy_1", "PBMC+SEB_DNAPKi_5Gy_1",
"PBMC+SEB_ATRi_0Gy_1", "PBMC+SEB_ATRi_5Gy_1", "PBMC-SEB_DMSO_0Gy_1",
"PBMC-SEB_DMSO_5Gy_1", "PBMC-SEB_ATMi_0Gy_1", "PBMC-SEB_ATMi_5Gy_1",
"PBMC-SEB_DNAPKi_0Gy_1", "PBMC-SEB_DNAPKi_5Gy_1", "PBMC-SEB_ATRi_0Gy_1",
"PBMC-SEB_ATRi_5Gy_1")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[2])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(37, 37))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 16)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 16)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file2
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file3 <- function()
{
message(sprintf("--- test_groupBoundaries_file3"))
expected.cols <- c("G7B_none_0Gy_1", "G7B_none_5Gy_1", "G7S_none_0Gy_1",
"G7S_none_5Gy_1", "G7S_ATMi_5Gy_1", "G7S_Olaparib_5Gy_1",
"R10B_none_0Gy_1", "R10B_none_5Gy_1", "R10S_none_0Gy_1",
"R10S_none_5Gy_1", "R10S_ATMi_5Gy_1", "R10S_Olaparib_5Gy_1")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[3])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(33, 29))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(tbl))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(tbl))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 12)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 12)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file3
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file4 <- function()
{
message(sprintf("--- test_groupBoundaries_file4"))
expected.cols <- c("LCL57_ATMi_0Gy_1", "LCL57_ATMi_5Gy_0.25", "LCL57_ATMi_5Gy_1",
"LCL57_ATMi_5Gy_6", "LCL57_ATMi_5Gy_24",
"LCL57_DMSO_0Gy_1", "LCL57_DMSO_5Gy_0.25", "LCL57_DMSO_5Gy_1",
"LCL57_DMSO_5Gy_6", "LCL57_DMSO_5Gy_24")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[4])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(37, 25))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(tbl))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(tbl))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 10)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 10)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file4
#----------------------------------------------------------------------------------------------------
test_getConditionFilenames <- function()
{
message(sprintf("--- test_getConditionFilenames"))
x <- ExcelProteomicsImporter(test.files[1])
colnames <- getConditionColnames(x)
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[1])),
c("LCL57_IR_00Gy_1","LCL57_IR_01Gy_1","LCL57_IR_02Gy_1","LCL57_IR_05Gy_1","LCL57_IR_10Gy_1"))
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[2])),
c("PBMC+SEB_DMSO_0Gy_1","PBMC+SEB_DMSO_5Gy_1","PBMC+SEB_ATMi_0Gy_1","PBMC+SEB_ATMi_5Gy_1",
"PBMC+SEB_DNAPKi_0Gy_1","PBMC+SEB_DNAPKi_5Gy_1","PBMC+SEB_ATRi_0Gy_1","PBMC+SEB_ATRi_5Gy_1",
"PBMC-SEB_DMSO_0Gy_1","PBMC-SEB_DMSO_5Gy_1","PBMC-SEB_ATMi_0Gy_1","PBMC-SEB_ATMi_5Gy_1",
"PBMC-SEB_DNAPKi_0Gy_1","PBMC-SEB_DNAPKi_5Gy_1","PBMC-SEB_ATRi_0Gy_1","PBMC-SEB_ATRi_5Gy_1"))
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[3])),
c("G7B_none_0Gy_1","G7B_none_5Gy_1","G7S_none_0Gy_1","G7S_none_5Gy_1","G7S_ATMi_5Gy_1",
"G7S_Olaparib_5Gy_1","R10B_none_0Gy_1","R10B_none_5Gy_1","R10S_none_0Gy_1",
"R10S_none_5Gy_1","R10S_ATMi_5Gy_1","R10S_Olaparib_5Gy_1"))
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[4])),
c("LCL57_ATMi_0Gy_1","LCL57_ATMi_5Gy_0.25","LCL57_ATMi_5Gy_1","LCL57_ATMi_5Gy_6",
"LCL57_ATMi_5Gy_24","LCL57_DMSO_0Gy_1","LCL57_DMSO_5Gy_0.25","LCL57_DMSO_5Gy_1",
"LCL57_DMSO_5Gy_6","LCL57_DMSO_5Gy_24"))
} # test_getConditionFilenames
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file1 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file1"))
x <- ExcelProteomicsImporter(test.files[1])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: LCL57_IR_00Gy_1")
checkEquals(yaml.lines[2], "sampleType: LCL57")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: IR")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: radiation")
checkEquals(yaml.lines[8], " level: 0.0")
checkEquals(yaml.lines[9], " units: Gy")
checkEquals(yaml.lines[10], "- name: time")
checkEquals(yaml.lines[11], " level: 1.0")
checkEquals(yaml.lines[12], " units: hours")
} # test_toYAMLreadyList_file1
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file2 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file2"))
x <- ExcelProteomicsImporter(test.files[2])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: PBMC+SEB_DMSO_0Gy_1")
checkEquals(yaml.lines[2], "sampleType: PBMC")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: SEB")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: DMSO")
checkEquals(yaml.lines[8], " level: ''")
checkEquals(yaml.lines[9], " units: ''")
checkEquals(yaml.lines[10], "- name: radiation")
checkEquals(yaml.lines[11], " level: 0.0")
checkEquals(yaml.lines[12], " units: Gy")
checkEquals(yaml.lines[13], "- name: time")
checkEquals(yaml.lines[14], " level: 1.0")
checkEquals(yaml.lines[15], " units: hours")
} # test_toYAMLreadyList_file2
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file3 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file3"))
x <- ExcelProteomicsImporter(test.files[3])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: G7B_none_0Gy_1")
checkEquals(yaml.lines[2], "sampleType: G7B")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: none")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: radiation")
checkEquals(yaml.lines[8], " level: 0.0")
checkEquals(yaml.lines[9], " units: Gy")
checkEquals(yaml.lines[10], "- name: time")
checkEquals(yaml.lines[11], " level: 1.0")
checkEquals(yaml.lines[12], " units: hours")
} # test_toYAMLreadyList_file3
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file4 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file4"))
x <- ExcelProteomicsImporter(test.files[4])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: LCL57_ATMi_0Gy_1")
checkEquals(yaml.lines[2], "sampleType: LCL57")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: ATMi")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: radiation")
checkEquals(yaml.lines[8], " level: 0.0")
checkEquals(yaml.lines[9], " units: Gy")
checkEquals(yaml.lines[10], "- name: time")
checkEquals(yaml.lines[11], " level: 1.0")
checkEquals(yaml.lines[12], " units: hours")
} # test_toYAMLreadyList_file4
#----------------------------------------------------------------------------------------------------
test_toYAML_file1 <- function()
{
message(sprintf("--- test_toYAML_file1"))
x <- ExcelProteomicsImporter(test.files[1])
list <- toYAML(x)
checkEquals(length(list$conditions), 5)
checkEquals(unlist(lapply(list$conditions, function(cond) cond$name)),
c("LfCL57_IR_00Gy_1", "LCL57_IR_01Gy_1", "LCL57_IR_02Gy_1", "LCL57_IR_05Gy_1", "LCL57_IR_10Gy_1"))
yaml.string <- as.yaml(list)
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[1])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file1
#----------------------------------------------------------------------------------------------------
test_toYAML_file2 <- function()
{
message(sprintf("--- test_toYAML_file2"))
x <- ExcelProteomicsImporter(test.files[2])
list <- toYAML(x)
checkEquals(length(list$conditions), 16)
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[2])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file2
#----------------------------------------------------------------------------------------------------
test_toYAML_file3 <- function()
{
message(sprintf("--- test_toYAML_file3"))
x <- ExcelProteomicsImporter(test.files[3])
list <- toYAML(x)
checkEquals(length(list$conditions), 12)
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[3])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file3
#----------------------------------------------------------------------------------------------------
test_toYAML_file4 <- function()
{
message(sprintf("--- test_toYAML_file4"))
x <- ExcelProteomicsImporter(test.files[4])
list <- toYAML(x)
checkEquals(length(list$conditions), 10)
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[4])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file4
#----------------------------------------------------------------------------------------------------
if(!interactive())
runTests()
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# test_ExcelProteomicsImporter.R
#------------------------------------------------------------------------------------------------------------------------
Sys.setlocale("LC_ALL", "C")
#------------------------------------------------------------------------------------------------------------------------
library(ExcelProteomicsImporter)
library(RUnit)
library(yaml)
#------------------------------------------------------------------------------------------------------------------------
test.files <- file.path(system.file(package="ExcelProteomicsImporter", "extdata"),
c("test_data2_LCL57cell_line_experiment2.txt",
"test_data3_PBMC_experiment.txt",
"test_data4_Glioma_cell_line_experiment.txt",
"test_data_LCL57cell_line_experiment_clean.txt"))
#------------------------------------------------------------------------------------------------------------------------
runTests <- function()
{
test_ctor()
test_validateColumnNames()
test_groupCount()
test_groupBoundaries_file1()
test_groupBoundaries_file2()
test_groupBoundaries_file3()
test_groupBoundaries_file4()
test_getConditionFilenames()
test_toYAMLreadyList_file1()
test_toYAMLreadyList_file2()
test_toYAMLreadyList_file3()
test_toYAMLreadyList_file4()
test_toYAML_file1()
test_toYAML_file2()
test_toYAML_file3()
test_toYAML_file4()
} # runTests
#------------------------------------------------------------------------------------------------------------------------
test_ctor <- function()
{
message(sprintf("--- test_ctor"))
for(file in test.files){
checkTrue(file.exists(file))
importer <- ExcelProteomicsImporter(file)
tbl.raw <- getRawTable(importer)
checkTrue(nrow(tbl.raw) %in% c(39, 37, 33, 37))
checkTrue(ncol(tbl.raw) %in% c(15, 37, 29, 25))
}
} # test_ctor
#------------------------------------------------------------------------------------------------------------------------
test_validateColumnNames <- function()
{
message(sprintf("--- test_validateColumnNames"))
for(file in test.files){
#printf("--- %s", file)
importer <- ExcelProteomicsImporter(file)
checkTrue(validateColumnNames(importer))
}
} # test_validateColumnNames
#------------------------------------------------------------------------------------------------------------------------
test_groupCount <- function()
{
message(sprintf("--- test_groupCount"))
# first file has just one group, so just one "avg" colname, one "stdev"
x <- ExcelProteomicsImporter(test.files[1])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
# second file has just one group, so just one "avg" colname, one "stdev"
x <- ExcelProteomicsImporter(test.files[2])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
# third file has just one group, so just one "avg" colname, one "stdev"
x <- ExcelProteomicsImporter(test.files[3])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
# fourth file has two groups, so two "avg" colnames, two "stdev"
x <- ExcelProteomicsImporter(test.files[4])
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
} # test_groupCount
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file1 <- function()
{
message(sprintf("--- test_groupBoundaries_file1"))
expected.cols <- c("LCL57_IR_00Gy_1", "LCL57_IR_01Gy_1", "LCL57_IR_02Gy_1", "LCL57_IR_05Gy_1", "LCL57_IR_10Gy_1")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[1])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(39, 15))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 5)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 5)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file1
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file2 <- function()
{
message(sprintf("--- test_groupBoundaries_file2"))
expected.cols <- c("PBMC+SEB_DMSO_0Gy_1", "PBMC+SEB_DMSO_5Gy_1", "PBMC+SEB_ATMi_0Gy_1",
"PBMC+SEB_ATMi_5Gy_1", "PBMC+SEB_DNAPKi_0Gy_1", "PBMC+SEB_DNAPKi_5Gy_1",
"PBMC+SEB_ATRi_0Gy_1", "PBMC+SEB_ATRi_5Gy_1", "PBMC-SEB_DMSO_0Gy_1",
"PBMC-SEB_DMSO_5Gy_1", "PBMC-SEB_ATMi_0Gy_1", "PBMC-SEB_ATMi_5Gy_1",
"PBMC-SEB_DNAPKi_0Gy_1", "PBMC-SEB_DNAPKi_5Gy_1", "PBMC-SEB_ATRi_0Gy_1",
"PBMC-SEB_ATRi_5Gy_1")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[2])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(37, 37))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(getRawTable(x)))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(getRawTable(x)))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 16)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 16)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file2
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file3 <- function()
{
message(sprintf("--- test_groupBoundaries_file3"))
expected.cols <- c("G7B_none_0Gy_1", "G7B_none_5Gy_1", "G7S_none_0Gy_1",
"G7S_none_5Gy_1", "G7S_ATMi_5Gy_1", "G7S_Olaparib_5Gy_1",
"R10B_none_0Gy_1", "R10B_none_5Gy_1", "R10S_none_0Gy_1",
"R10S_none_5Gy_1", "R10S_ATMi_5Gy_1", "R10S_Olaparib_5Gy_1")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[3])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(33, 29))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(tbl))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(tbl))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 12)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 12)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file3
#------------------------------------------------------------------------------------------------------------------------
test_groupBoundaries_file4 <- function()
{
message(sprintf("--- test_groupBoundaries_file4"))
expected.cols <- c("LCL57_ATMi_0Gy_1", "LCL57_ATMi_5Gy_0.25", "LCL57_ATMi_5Gy_1",
"LCL57_ATMi_5Gy_6", "LCL57_ATMi_5Gy_24",
"LCL57_DMSO_0Gy_1", "LCL57_DMSO_5Gy_0.25", "LCL57_DMSO_5Gy_1",
"LCL57_DMSO_5Gy_6", "LCL57_DMSO_5Gy_24")
#-------------------------------------------------------------------------
# first file has just one group, so just one "avg" colname, one "stdev"
#-------------------------------------------------------------------------
x <- ExcelProteomicsImporter(test.files[4])
tbl <- getRawTable(x)
checkEquals(dim(tbl), c(37, 25))
checkEquals(getGroupCount(x), 1)
checkEquals(length(grep("avg", colnames(tbl))), getGroupCount(x))
checkEquals(length(grep("stdev", colnames(tbl))), getGroupCount(x))
#--------------------------------------------------------------------------------
# one good test: avg colnames match stdev colnames, with latter having .1 suffix
#--------------------------------------------------------------------------------
cols <- getGroupBoundaries(x)
avg.cols <- colnames(tbl)[cols$avg.1[1]: cols$avg.1[2]]
checkEquals(length(avg.cols), 10)
checkEquals(avg.cols, expected.cols)
stdev.cols <- colnames(tbl)[cols$sd.1[1]: cols$sd.1[2]]
checkEquals(length(stdev.cols), 10)
checkEquals(stdev.cols, expected.cols)
} # test_groupBoundaries_file4
#----------------------------------------------------------------------------------------------------
test_getConditionFilenames <- function()
{
message(sprintf("--- test_getConditionFilenames"))
x <- ExcelProteomicsImporter(test.files[1])
colnames <- getConditionColnames(x)
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[1])),
c("LCL57_IR_00Gy_1","LCL57_IR_01Gy_1","LCL57_IR_02Gy_1","LCL57_IR_05Gy_1","LCL57_IR_10Gy_1"))
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[2])),
c("PBMC+SEB_DMSO_0Gy_1","PBMC+SEB_DMSO_5Gy_1","PBMC+SEB_ATMi_0Gy_1","PBMC+SEB_ATMi_5Gy_1",
"PBMC+SEB_DNAPKi_0Gy_1","PBMC+SEB_DNAPKi_5Gy_1","PBMC+SEB_ATRi_0Gy_1","PBMC+SEB_ATRi_5Gy_1",
"PBMC-SEB_DMSO_0Gy_1","PBMC-SEB_DMSO_5Gy_1","PBMC-SEB_ATMi_0Gy_1","PBMC-SEB_ATMi_5Gy_1",
"PBMC-SEB_DNAPKi_0Gy_1","PBMC-SEB_DNAPKi_5Gy_1","PBMC-SEB_ATRi_0Gy_1","PBMC-SEB_ATRi_5Gy_1"))
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[3])),
c("G7B_none_0Gy_1","G7B_none_5Gy_1","G7S_none_0Gy_1","G7S_none_5Gy_1","G7S_ATMi_5Gy_1",
"G7S_Olaparib_5Gy_1","R10B_none_0Gy_1","R10B_none_5Gy_1","R10S_none_0Gy_1",
"R10S_none_5Gy_1","R10S_ATMi_5Gy_1","R10S_Olaparib_5Gy_1"))
checkEquals(getConditionColnames(ExcelProteomicsImporter(test.files[4])),
c("LCL57_ATMi_0Gy_1","LCL57_ATMi_5Gy_0.25","LCL57_ATMi_5Gy_1","LCL57_ATMi_5Gy_6",
"LCL57_ATMi_5Gy_24","LCL57_DMSO_0Gy_1","LCL57_DMSO_5Gy_0.25","LCL57_DMSO_5Gy_1",
"LCL57_DMSO_5Gy_6","LCL57_DMSO_5Gy_24"))
} # test_getConditionFilenames
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file1 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file1"))
x <- ExcelProteomicsImporter(test.files[1])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: LCL57_IR_00Gy_1")
checkEquals(yaml.lines[2], "sampleType: LCL57")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: IR")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: radiation")
checkEquals(yaml.lines[8], " level: 0.0")
checkEquals(yaml.lines[9], " units: Gy")
checkEquals(yaml.lines[10], "- name: time")
checkEquals(yaml.lines[11], " level: 1.0")
checkEquals(yaml.lines[12], " units: hours")
} # test_toYAMLreadyList_file1
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file2 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file2"))
x <- ExcelProteomicsImporter(test.files[2])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: PBMC+SEB_DMSO_0Gy_1")
checkEquals(yaml.lines[2], "sampleType: PBMC")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: SEB")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: DMSO")
checkEquals(yaml.lines[8], " level: ''")
checkEquals(yaml.lines[9], " units: ''")
checkEquals(yaml.lines[10], "- name: radiation")
checkEquals(yaml.lines[11], " level: 0.0")
checkEquals(yaml.lines[12], " units: Gy")
checkEquals(yaml.lines[13], "- name: time")
checkEquals(yaml.lines[14], " level: 1.0")
checkEquals(yaml.lines[15], " units: hours")
} # test_toYAMLreadyList_file2
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file3 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file3"))
x <- ExcelProteomicsImporter(test.files[3])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: G7B_none_0Gy_1")
checkEquals(yaml.lines[2], "sampleType: G7B")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: none")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: radiation")
checkEquals(yaml.lines[8], " level: 0.0")
checkEquals(yaml.lines[9], " units: Gy")
checkEquals(yaml.lines[10], "- name: time")
checkEquals(yaml.lines[11], " level: 1.0")
checkEquals(yaml.lines[12], " units: hours")
} # test_toYAMLreadyList_file3
#----------------------------------------------------------------------------------------------------
test_toYAMLreadyList_file4 <- function()
{
message(sprintf("--- test_toYAMLreadyList_file4"))
x <- ExcelProteomicsImporter(test.files[4])
colnames <- getConditionColnames(x)
yaml.string <- as.yaml(conditionToYAMLreadyList(x, colnames[1]))
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
checkEquals(yaml.lines[1], "name: LCL57_ATMi_0Gy_1")
checkEquals(yaml.lines[2], "sampleType: LCL57")
checkEquals(yaml.lines[3], "treatments:")
checkEquals(yaml.lines[4], "- name: ATMi")
checkEquals(yaml.lines[5], " level: ''")
checkEquals(yaml.lines[6], " units: ''")
checkEquals(yaml.lines[7], "- name: radiation")
checkEquals(yaml.lines[8], " level: 0.0")
checkEquals(yaml.lines[9], " units: Gy")
checkEquals(yaml.lines[10], "- name: time")
checkEquals(yaml.lines[11], " level: 1.0")
checkEquals(yaml.lines[12], " units: hours")
} # test_toYAMLreadyList_file4
#----------------------------------------------------------------------------------------------------
test_toYAML_file1 <- function()
{
message(sprintf("--- test_toYAML_file1"))
x <- ExcelProteomicsImporter(test.files[1])
list <- toYAML(x)
checkEquals(length(list$conditions), 5)
checkEquals(unlist(lapply(list$conditions, function(cond) cond$name)),
c("LfCL57_IR_00Gy_1", "LCL57_IR_01Gy_1", "LCL57_IR_02Gy_1", "LCL57_IR_05Gy_1", "LCL57_IR_10Gy_1"))
yaml.string <- as.yaml(list)
yaml.lines <- strsplit(yaml.string, "\n")[[1]]
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[1])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file1
#----------------------------------------------------------------------------------------------------
test_toYAML_file2 <- function()
{
message(sprintf("--- test_toYAML_file2"))
x <- ExcelProteomicsImporter(test.files[2])
list <- toYAML(x)
checkEquals(length(list$conditions), 16)
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[2])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file2
#----------------------------------------------------------------------------------------------------
test_toYAML_file3 <- function()
{
message(sprintf("--- test_toYAML_file3"))
x <- ExcelProteomicsImporter(test.files[3])
list <- toYAML(x)
checkEquals(length(list$conditions), 12)
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[3])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file3
#----------------------------------------------------------------------------------------------------
test_toYAML_file4 <- function()
{
message(sprintf("--- test_toYAML_file4"))
x <- ExcelProteomicsImporter(test.files[4])
list <- toYAML(x)
checkEquals(length(list$conditions), 10)
yaml.out <- sprintf("%s.yaml", sub(".txt", "", basename(test.files[4])))
writeLines(yaml.lines, yaml.out)
} # test_toYAML_file4
#----------------------------------------------------------------------------------------------------
if(!interactive())
runTests()
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