inst/unitTests/test_readNanoStringRccSet.R
In Nanostring-Biostats/NanoStringNCTools: NanoString nCounter Tools
test_readNanoStringRccSet_onearg <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE))
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
IsControl = c(FALSE, FALSE),
ControlConc = c(NA_real_, NA_real_),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),])
checkIdentical(data.frame(FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
test_readNanoStringRccSet_rlf <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE),
file.path(datadir, "3D_SolidTumor_Sig.rlf"))
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
IsControl = c(FALSE, FALSE),
ControlConc = c(NA_real_, NA_real_),
Barcode = c("BGBGYR", "YRGRYR"),
ProbeID = c("NM_000546.2:1330", "nRef_00032:1"),
Species = c("Hs", "Hs"),
BarcodeComments = c("ENDOGENOUS", "SNV_REF"),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),
c("CodeClass", "GeneName", "Accession",
"IsControl", "ControlConc",
"Barcode", "ProbeID", "Species",
"BarcodeComments")])
checkIdentical(data.frame(FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
test_readNanoStringRccSet_rlf_pheno <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE),
file.path(datadir, "3D_SolidTumor_Sig.rlf"),
file.path(datadir, "3D_SolidTumor_PhenoData.csv"))
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
Barcode = c("BGBGYR", "YRGRYR"),
ProbeID = c("NM_000546.2:1330", "nRef_00032:1"),
Species = c("Hs", "Hs"),
BarcodeComments = c("ENDOGENOUS", "SNV_REF"),
IsControl = c(FALSE, FALSE),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),
c("CodeClass", "GeneName", "Accession",
"Barcode", "ProbeID", "Species",
"BarcodeComments", "IsControl")])
checkIdentical(data.frame(Treatment = c("DMSO", "VEM"),
BRAFGenotype = c("wt/wt", "mut/mut"),
FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
test_readNanoStringRccSet_rlf_pheno <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE),
file.path(datadir, "3D_SolidTumor_Sig.rlf"),
file.path(datadir, "3D_SolidTumor_PhenoData.csv"),
phenoDataColPrefix = "PHENO_")
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
Barcode = c("BGBGYR", "YRGRYR"),
ProbeID = c("NM_000546.2:1330", "nRef_00032:1"),
Species = c("Hs", "Hs"),
BarcodeComments = c("ENDOGENOUS", "SNV_REF"),
IsControl = c(FALSE, FALSE),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),
c("CodeClass", "GeneName", "Accession",
"Barcode", "ProbeID", "Species",
"BarcodeComments", "IsControl")])
checkIdentical(data.frame(PHENO_Treatment = c("DMSO", "VEM"),
PHENO_BRAFGenotype = c("wt/wt", "mut/mut"),
FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
Nanostring-Biostats/NanoStringNCTools documentation built on April 19, 2024, 8:21 p.m.
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test_readNanoStringRccSet_onearg <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE))
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
IsControl = c(FALSE, FALSE),
ControlConc = c(NA_real_, NA_real_),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),])
checkIdentical(data.frame(FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
test_readNanoStringRccSet_rlf <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE),
file.path(datadir, "3D_SolidTumor_Sig.rlf"))
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
IsControl = c(FALSE, FALSE),
ControlConc = c(NA_real_, NA_real_),
Barcode = c("BGBGYR", "YRGRYR"),
ProbeID = c("NM_000546.2:1330", "nRef_00032:1"),
Species = c("Hs", "Hs"),
BarcodeComments = c("ENDOGENOUS", "SNV_REF"),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),
c("CodeClass", "GeneName", "Accession",
"IsControl", "ControlConc",
"Barcode", "ProbeID", "Species",
"BarcodeComments")])
checkIdentical(data.frame(FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
test_readNanoStringRccSet_rlf_pheno <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE),
file.path(datadir, "3D_SolidTumor_Sig.rlf"),
file.path(datadir, "3D_SolidTumor_PhenoData.csv"))
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
Barcode = c("BGBGYR", "YRGRYR"),
ProbeID = c("NM_000546.2:1330", "nRef_00032:1"),
Species = c("Hs", "Hs"),
BarcodeComments = c("ENDOGENOUS", "SNV_REF"),
IsControl = c(FALSE, FALSE),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),
c("CodeClass", "GeneName", "Accession",
"Barcode", "ProbeID", "Species",
"BarcodeComments", "IsControl")])
checkIdentical(data.frame(Treatment = c("DMSO", "VEM"),
BRAFGenotype = c("wt/wt", "mut/mut"),
FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
test_readNanoStringRccSet_rlf_pheno <- function() {
datadir <- system.file("extdata", "3D_Bio_Example_Data",
package = "NanoStringNCTools")
rcc <-
readNanoStringRccSet(dir(datadir, pattern = "SKMEL.*\\.RCC$",
full.names = TRUE),
file.path(datadir, "3D_SolidTumor_Sig.rlf"),
file.path(datadir, "3D_SolidTumor_PhenoData.csv"),
phenoDataColPrefix = "PHENO_")
checkTrue(validObject(rcc))
checkIdentical(c(Features = 397L, Samples = 12L), dim(rcc))
checkIdentical(data.frame(CodeClass = c("Endogenous", "SNV_REF"),
GeneName =
c("TP53",
"PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141"),
Accession = c("NM_000546.2", "nRef_00032.1"),
Barcode = c("BGBGYR", "YRGRYR"),
ProbeID = c("NM_000546.2:1330", "nRef_00032:1"),
Species = c("Hs", "Hs"),
BarcodeComments = c("ENDOGENOUS", "SNV_REF"),
IsControl = c(FALSE, FALSE),
row.names =
c("Endogenous_TP53_NM_000546.2",
"SNV_REF_PIK3CA Ref (exon 10)|hg19|+|chr3:178936060-178936141_nRef_00032.1"),
stringsAsFactors = FALSE),
fData(rcc)[c(1L, nrow(rcc)),
c("CodeClass", "GeneName", "Accession",
"Barcode", "ProbeID", "Species",
"BarcodeComments", "IsControl")])
checkIdentical(data.frame(PHENO_Treatment = c("DMSO", "VEM"),
PHENO_BRAFGenotype = c("wt/wt", "mut/mut"),
FileVersion = numeric_version(c("1.7", "1.7")),
SoftwareVersion = numeric_version(c("4.0.0.3", "4.0.0.3")),
SystemType = c("Gen2", "Gen2"),
SampleID = c("SKMEL2-DMSO-8hr", "SKMEL28-V-8hr"),
SampleOwner = c("", ""),
SampleComments = c("DNA-RNA-Protein", "DNA-RNA-Protein"),
SampleDate = as.Date(c("2017-01-13", "2017-01-25")),
SystemAPF = c("n6_vDV1", "n6_vDV1"),
AssayType = c(NA_character_, NA_character_),
LaneID = c(4L, 10L),
FovCount = c(280L, 280L),
FovCounted = c(268L, 279L),
ScannerID = c("1207C0049", "1207C0049"),
StagePosition = c(3L, 3L),
BindingDensity = c(0.8, 0.64),
CartridgeID = c("AGBT-3DBio-C1-SKMEL2",
"AGBT-3DBio-2-Repeat-C3-SKMEL28"),
CartridgeBarcode = c("", ""),
row.names = c("SKMEL2-DMSO-8h-R1_04.RCC",
"SKMEL28-VEM-8h-R3_10.RCC"),
stringsAsFactors = FALSE),
sData(rcc)[c(1L, ncol(rcc)),])
}
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