methods::getClass("DESeqDataSet")@contains # 应包含"ExpData"
$RangedSummarizedExperiment
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
value <- methods::new("RangedSummarizedExperiment")
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(value, what) <- methods::slot(from,
what)
value
}
<bytecode: 0x0000020b35726ed0>
<environment: namespace:DESeq2>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b35725f10>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
<bytecode: 0x0000020b35725d88>
<environment: namespace:DESeq2>
Slot "simple":
[1] TRUE
Slot "by":
character(0)
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 1
$SummarizedExperiment
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "SummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
from <- {
value <- methods::new("RangedSummarizedExperiment")
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(value,
what) <- methods::slot(from, what)
value
}
{
value <- methods::new("SummarizedExperiment")
for (what in c("colData", "assays", "NAMES", "elementMetadata",
"metadata")) methods::slot(value, what) <- methods::slot(from,
what)
value
}
}
<bytecode: 0x0000020b3572cbf0>
<environment: namespace:SummarizedExperiment>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b3572b728>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
.value <- methods::as(from, "RangedSummarizedExperiment",
TRUE)
methods::as(.value, "SummarizedExperiment") <- value
value <- .value
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
}
<bytecode: 0x0000020b3572b5a0>
<environment: namespace:DESeq2>
Slot "simple":
[1] TRUE
Slot "by":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 2
$RectangularData
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "RectangularData"
attr(,"package")
[1] "S4Vectors"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
from <- {
value <- methods::new("RangedSummarizedExperiment")
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(value,
what) <- methods::slot(from, what)
value
}
{
from <- {
value <- methods::new("SummarizedExperiment")
for (what in c("colData", "assays", "NAMES", "elementMetadata",
"metadata")) methods::slot(value, what) <- methods::slot(from,
what)
value
}
from
}
}
<bytecode: 0x0000020b3572ff60>
<environment: namespace:methods>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b357328d8>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
.value <- methods::as(from, "RangedSummarizedExperiment",
TRUE)
methods::as(.value, "RectangularData") <- value
value <- .value
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
}
<bytecode: 0x0000020b35732750>
<environment: namespace:DESeq2>
Slot "simple":
[1] TRUE
Slot "by":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 3
$Vector
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "Vector"
attr(,"package")
[1] "S4Vectors"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
from <- {
value <- methods::new("RangedSummarizedExperiment")
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(value,
what) <- methods::slot(from, what)
value
}
{
from <- {
value <- methods::new("SummarizedExperiment")
for (what in c("colData", "assays", "NAMES", "elementMetadata",
"metadata")) methods::slot(value, what) <- methods::slot(from,
what)
value
}
from
}
}
<bytecode: 0x0000020b357311e0>
<environment: namespace:methods>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b3572dbd0>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
.value <- methods::as(from, "RangedSummarizedExperiment",
TRUE)
methods::as(.value, "Vector") <- value
value <- .value
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
}
<bytecode: 0x0000020b3572da48>
<environment: namespace:DESeq2>
Slot "simple":
[1] TRUE
Slot "by":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 3
$ExpData
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "ExpData"
attr(,"package")
[1] "SummarizedExperiment"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
from <- as(from, "RangedSummarizedExperiment", strict = strict)
{
from <- as(from, "SummarizedExperiment", strict = strict)
from
}
}
<bytecode: 0x0000020b35736428>
<environment: namespace:methods>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b35735c80>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
.value <- methods::as(from, "RangedSummarizedExperiment",
TRUE)
methods::as(.value, "ExpData") <- value
value <- .value
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
}
<bytecode: 0x0000020b35735af8>
<environment: namespace:DESeq2>
Slot "simple":
[1] FALSE
Slot "by":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 3
$Annotated
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "Annotated"
attr(,"package")
[1] "S4Vectors"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
from <- {
value <- methods::new("RangedSummarizedExperiment")
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(value,
what) <- methods::slot(from, what)
value
}
{
from <- {
value <- methods::new("SummarizedExperiment")
for (what in c("colData", "assays", "NAMES", "elementMetadata",
"metadata")) methods::slot(value, what) <- methods::slot(from,
what)
value
}
from
}
}
<bytecode: 0x0000020b357384a8>
<environment: namespace:methods>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b35740e18>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
.value <- methods::as(from, "RangedSummarizedExperiment",
TRUE)
methods::as(.value, "Annotated") <- value
value <- .value
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
}
<bytecode: 0x0000020b35740c90>
<environment: namespace:DESeq2>
Slot "simple":
[1] TRUE
Slot "by":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 4
$vector_OR_Vector
An object of class "SClassExtension"
Slot "subClass":
[1] "DESeqDataSet"
attr(,"package")
[1] "DESeq2"
Slot "superClass":
[1] "vector_OR_Vector"
attr(,"package")
[1] "S4Vectors"
Slot "package":
[1] "DESeq2"
Slot "coerce":
function (from, strict = TRUE)
{
from <- {
value <- methods::new("RangedSummarizedExperiment")
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(value,
what) <- methods::slot(from, what)
value
}
{
from <- {
value <- methods::new("SummarizedExperiment")
for (what in c("colData", "assays", "NAMES", "elementMetadata",
"metadata")) methods::slot(value, what) <- methods::slot(from,
what)
value
}
from
}
}
<bytecode: 0x0000020b3573f720>
<environment: namespace:methods>
Slot "test":
function (object)
TRUE
<bytecode: 0x0000020b3573a100>
<environment: namespace:methods>
Slot "replace":
function (from, to, value)
{
.value <- methods::as(from, "RangedSummarizedExperiment",
TRUE)
methods::as(.value, "vector_OR_Vector") <- value
value <- .value
{
for (what in c("rowRanges", "colData", "assays", "NAMES",
"elementMetadata", "metadata")) methods::slot(from, what) <- methods::slot(value,
what)
from
}
}
<bytecode: 0x0000020b35739f78>
<environment: namespace:DESeq2>
Slot "simple":
[1] TRUE
Slot "by":
[1] "RangedSummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"
Slot "dataPart":
[1] FALSE
Slot "distance":
[1] 4
本文记录了在使用 Oracle 数据库进行数据导出时遇到的问题及解决过程。通过调整 shell 脚本中的参数设置，解决了多次出现的错误，并最终成功完成了数据导出任务。
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