nuget
A Replicate object represents information about a single RNA-seq experiment, including information about all reads from the experiment.
Replicate
01 Syntax
SMRUCC.genomics.SequenceModel.RNA_Seq.Rockhopper.Core.Replicate
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | Constructs a new Replicate object based on compressed sequencing reads. |
| GetCompressedFileName | 1 | Return the name of the compressed alignment file for this Replicate for the specified genome at index z. |
| GetReads | 1 | Return the number of reads mapping to the specified coordinate on the specified strand for the specified genome at index z. |
| GetReadsInRange | 1 | Return the number of reads on the given strand mapping to the given range of genomic coordinates for the specified genome at index z. |
| GetBackgroundProb | 1 | Returns the probability that the given number of reads at some nucleotide corresponds to the background, i.e., a non-transcript. |
| GetMeanOfRange | 1 | Return the mean number of reads on the given strand mapping to the given range of genomic coordinates in the specified genome at index z. |
| GetStdevOfRange | 1 | Return the standard deviation of reads on the given strand mapping to the given range of genomic coordinates in the specified genome at index z. |
| transformation | 1 | Helper method for setting the minimum expression level for UTRs and ncRNAs. |
| ToString | 1 | Returns a String representation of this object. |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| TotalReads | 1 | Return total number of reads in this Replicate. |
| AvgReads | 1 | Return average number of reads per nucleotide in this Replicate. |
| AvgLengthReads | 1 | Return average length of sequencing reads in this Replicate. |
| UpperQuartile | 1 | Return the upper quartile for this Replicate. |
| MinExpression | 1 | Sets the minimum level of expression (for a UTR region and ncRNA to be considered expressed) based on the average number of reads per nucleotide and the specified transcript sens… |
| MinExpressionUTR | 1 | Return the minimum expression for a UTR region. |
| MinExpressionRNA | 1 | Return the minimum expression for a ncRNA. |
| Name | 1 |
04 Fields
| Name | Overloads | Summary |
|---|---|---|
| fileName | 1 | 原始读段文件路径。 |
| compressedFileNames | 1 | 每个复制子的压缩文件名。 |
| plusReads | 1 | 正链读段数，[genome][coordinate]。 |
| minusReads | 1 | 负链读段数，[genome][coordinate]。 |
| _avgLengthReads | 1 | 平均读长。 |
| genomeSizes | 1 | 每个复制子的长度。 |
| genomeSize | 1 | 全部复制子长度之和。 |
| background | 1 | Number of nucleotides with few or no reads. |
| backgroundParameter | 1 | Parameter of geometric distribution of background reads. |
| _avgReads | 1 | Average number of reads mapping to nucleotides throughout genome. |
| _minExpressionUTR | 1 | Minimum expression for a UTR region to be deemed expressed. |
| _minExpressionRNA | 1 | Minimum expression for a ncRNA to be deemed expressed. |
| _name | 1 | 实验名称（由读段文件名推断）。 |
05 Members
#ctor(AlignmentCoverage(),
Boolean)Constructs a new Replicate object based on compressed sequencing reads.
Parameters
| Name | Type | Description |
|---|---|---|
coverages | AlignmentCoverage() | 每个复制子对应的覆盖度数据。 |
unstranded | Boolean | 是否为链非特异（模糊链）数据。 |
GetCompressedFileName(
Int32)Return the name of the compressed alignment file for this Replicate for the specified genome at index z.
GetReads(
Int32, Int32, Char)Return the number of reads mapping to the specified coordinate on the specified strand for the specified genome at index z.
GetReadsInRange(
Int32, Int32, Int32, Char)Return the number of reads on the given strand mapping to the given range of genomic coordinates for the specified genome at index z.
GetBackgroundProb(
Int32)Returns the probability that the given number of reads at some nucleotide corresponds to the background, i.e., a non-transcript.
GetMeanOfRange(
Int32, Int32, Int32, Char)Return the mean number of reads on the given strand mapping to the given range of genomic coordinates in the specified genome at index z.
GetStdevOfRange(
Int32, Int32, Int32, Char, Double)Return the standard deviation of reads on the given strand mapping to the given range of genomic coordinates in the specified genome at index z.
transformation(
Double)Helper method for setting the minimum expression level for UTRs and ncRNAs.
ToString
Returns a String representation of this object.
TotalReads
Return total number of reads in this Replicate.
AvgReads
Return average number of reads per nucleotide in this Replicate.
AvgLengthReads
Return average length of sequencing reads in this Replicate.
UpperQuartile
Return the upper quartile for this Replicate.
MinExpression
Sets the minimum level of expression (for a UTR region and ncRNA to be considered expressed) based on the average number of reads per nucleotide and the specified transcript sensitivity in [0.0, 1.0].
MinExpressionUTR
Return the minimum expression for a UTR region.
MinExpressionRNA
Return the minimum expression for a ncRNA.
fileName
原始读段文件路径。
compressedFileNames
每个复制子的压缩文件名。
plusReads
正链读段数，[genome][coordinate]。
minusReads
负链读段数，[genome][coordinate]。
_avgLengthReads
平均读长。
genomeSizes
每个复制子的长度。
genomeSize
全部复制子长度之和。
background
Number of nucleotides with few or no reads.
backgroundParameter
Parameter of geometric distribution of background reads.
_avgReads
Average number of reads mapping to nucleotides throughout genome.
_minExpressionUTR
Minimum expression for a UTR region to be deemed expressed.
_minExpressionRNA
Minimum expression for a ncRNA to be deemed expressed.
_name
实验名称（由读段文件名推断）。
Name