nuget
A Gene object represents a gene (either protein-coding or RNA). A Gene object consists of a variety of data about a gene, including its coordinates, strand, name, product, and expression information in each replicate (raw counts mapping to gene and normalized counts mapping to gene) or in each condition (mean, variance, lowess, RPKM) or in a pair of conditions (p-value of differential expression).
Gene
01 Syntax
SMRUCC.genomics.SequenceModel.RNA_Seq.Rockhopper.Core.Gene
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | Constructs a new Gene object based on a line from a gene file (either *.ptt or *.rnt). |
| GetRawCount | 1 | Return the number of reads mapping to the gene in the specified condition and replicate. |
| GetRawCount_reads | 1 | Return the number of reads (read-level) mapping to the gene. |
| GetNormalizedCount | 1 | Return the normalized number of reads mapping to the gene. |
| GetMean | 1 | Return the mean reads mapping to the gene in the specified condition. |
| GetAvg | 1 | Returns the average expression of the gene (averaged over the length of the gene) in the specified condition. |
| GetRPKM | 1 | Return the RPKM value of this gene in the specified condition. |
| GetNumReplicates | 1 | Return the number of replicates in the specified condition. |
| ExpressionToString | 1 | Returns a String representation of a Gene's expression in each condition and p-values of differential expression. |
| ensureCapacity | 1 | 确保 expression 数据容器已扩展到 [condition][replicate] 维度。 |
| SetRawCount | 1 | Set the number of reads mapping to this Gene in the specified replicate in the specified condition. |
| SetRawCount_reads | 1 | Set the read-level number of reads mapping to this Gene. |
| SetNormalizedCount | 1 | Set the normalized number of reads mapping to this Gene. |
| ComputeExpression | 1 | For each condition, across all replicates of the conditions, compute the mean and RPKM for this Gene. |
| ComputeVariance | 1 | For each condition, across all replicates of the conditions, compute the variance for this Gene. |
| ComputeDifferentialExpression | 1 | For each pair of conditions, compute the p-value of differential expression for this Gene. |
| IsDifferentiallyExpressedORF | 1 | Returns true if this Gene is an ORF and if it is differentially expressed in at least one pair of conditions at the specified significance level. |
| SetLowessVariances | 1 | Computes the Lowess variance for each Gene in the Genome. |
| CorrectPvalues | 1 | Computes q-values for each gene, i.e., corrected p-values, using Benjamini Hochberg correction. |
| ToString | 1 | Returns a String representation of a Gene. |
| HasQvalue | 1 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| Start | 1 | 翻译起始位点（Translation start）。 |
| Stop | 1 | 翻译终止位点（Translation stop）。 |
| Strand | 1 | 基因所在链，'+' / '-' / '?'。 |
| Type | 1 | 基因类型，ORF 或 RNA。 |
| ID | 1 | 基因 ID（GenBank 中的 PID）。 |
| Name | 1 | 基因名（GenBank 中的 gene name）。 |
| Synonym | 1 | 基因别名 / locus_tag。 |
| Product | 1 | 基因产物描述。 |
| StartT | 1 | 转录起始位点（Transcription start），RNA 基因由注释给出，ORF 由预测给出。 |
| StopT | 1 | 转录终止位点（Transcription stop）。 |
| ORF | 1 | Returns true if this gene is a protein coding gene, false otherwise. |
| First | 1 | Returns the first (smallest) coordinate of this Gene. |
| Last | 1 | Returns the last (largest) coordinate of this Gene. |
| MinCoordinate | 1 | Returns the coordinate (among transcription start/stop coordinates and translation start/stop coordinates) with minimum value. |
| MaxCoordinate | 1 | Returns the coordinate with maximum value. |
| MinQvalue | 1 | Returns the minimum q-value for this Gene. |
04 Fields
| Name | Overloads | Summary |
|---|---|---|
| rawCounts | 2 | 每个碱基上比对的读段数，[condition][replicate][coordinate]。 |
| rawCounts_reads | 2 | 比对到基因上的读段数（不展开到每个碱基），[condition][replicate]。 |
| pValues | 2 | 差异表达 p 值（按条件对的顺序排列）。 |
| qValues | 2 | 差异表达 q 值（BH 校正后）。 |
05 Members
#ctor(
String, String)Constructs a new Gene object based on a line from a gene file (either .ptt or .rnt).
Parameters
| Name | Type | Description |
|---|---|---|
line | String | .ptt / .rnt 中的一行（Tab 分隔，至少 9 列）。 |
type | String | ORF 或 RNA。 |
GetRawCount(
Int32, Int32)Return the number of reads mapping to the gene in the specified condition and replicate.
GetRawCount_reads(
Int32, Int32)Return the number of reads (read-level) mapping to the gene.
GetNormalizedCount(
Int32, Int32)Return the normalized number of reads mapping to the gene.
GetMean(
Int32)Return the mean reads mapping to the gene in the specified condition.
GetAvg(
Int32)Returns the average expression of the gene (averaged over the length of the gene) in the specified condition.
GetRPKM(
Int32)Return the RPKM value of this gene in the specified condition.
GetNumReplicates(
Int32)Return the number of replicates in the specified condition.
ExpressionToString
Returns a String representation of a Gene's expression in each condition and p-values of differential expression.
ensureCapacity(
Int32, Int32)确保 expression 数据容器已扩展到 [condition][replicate] 维度。
SetRawCount(
Int32, Int32, Int64)Set the number of reads mapping to this Gene in the specified replicate in the specified condition.
SetRawCount_reads(
Int32, Int32, Int64)Set the read-level number of reads mapping to this Gene.
SetNormalizedCount(
Int32, Int32, Double, Int64)Set the normalized number of reads mapping to this Gene.
ComputeExpression(
List(Of Condition))For each condition, across all replicates of the conditions, compute the mean and RPKM for this Gene.
ComputeVariance(
List(Of Condition))For each condition, across all replicates of the conditions, compute the variance for this Gene.
ComputeDifferentialExpression
For each pair of conditions, compute the p-value of differential expression for this Gene.
IsDifferentiallyExpressedORF(
Double)Returns true if this Gene is an ORF and if it is differentially expressed in at least one pair of conditions at the specified significance level.
SetLowessVariances(
List(Of Genome), List(Of Condition))Computes the Lowess variance for each Gene in the Genome.
CorrectPvalues(
List(Of Genome), List(Of Condition))Computes q-values for each gene, i.e., corrected p-values, using Benjamini Hochberg correction.
ToString
Returns a String representation of a Gene.
Start
翻译起始位点（Translation start）。
Stop
翻译终止位点（Translation stop）。
Strand
基因所在链，'+' / '-' / '?'。
Type
基因类型，ORF 或 RNA。
ID
基因 ID（GenBank 中的 PID）。
Name
基因名（GenBank 中的 gene name）。
Synonym
基因别名 / locus_tag。
Product
基因产物描述。
StartT
转录起始位点（Transcription start），RNA 基因由注释给出，ORF 由预测给出。
StopT
转录终止位点（Transcription stop）。
ORF
Returns true if this gene is a protein coding gene, false otherwise.
First
Returns the first (smallest) coordinate of this Gene. If this Gene is an ORF it returns the smallest translation coordinate. If this Gene is an RNA it returns the smallest transcription coordinate.
Last
Returns the last (largest) coordinate of this Gene.
MinCoordinate
Returns the coordinate (among transcription start/stop coordinates and translation start/stop coordinates) with minimum value.
MaxCoordinate
Returns the coordinate with maximum value.
MinQvalue
Returns the minimum q-value for this Gene.
rawCounts
每个碱基上比对的读段数，[condition][replicate][coordinate]。
rawCounts_reads
比对到基因上的读段数（不展开到每个碱基），[condition][replicate]。
pValues
差异表达 p 值（按条件对的顺序排列）。
qValues
差异表达 q 值（BH 校正后）。
rawCounts
rawCounts_reads
pValues
qValues
HasQvalue(
Int32)