SequenceMatrix

Full name SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.Matrix.SequenceMatrix Assembly SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifFinder Members 5

01 Syntax

SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.Matrix.SequenceMatrix

02 Methods

Name	Overloads	Summary
initSequenceMatrix	1	Counts the occurrences of each base along each position of each sequence
observedCount	1	第 index 列之上实际观测到的碱基数量（被屏蔽为 N 的位置不计入）
probability	1	Returns the probability of seeing the base in the index

03 Fields

Name	Overloads	Summary
PSEUDOCOUNT	1	加一平滑所引入的伪计数
columnObserved	1	每一列之上实际观测到的碱基数量，N 等非标准字符不计入

04 Members

method initSequenceMatrix #

initSequenceMatrix

Counts the occurrences of each base along each position of each sequence

method observedCount #

observedCount(Int32)

第 index 列之上实际观测到的碱基数量（被屏蔽为 N 的位置不计入）

Parameters

Name	Type	Description
`index`	`Int32`	, index of base

method probability #

probability(Int32, Int32)

Returns the probability of seeing the base in the index

Parameters

Name	Type	Description
`index`	`Int32`	, index of base
`base`	`Int32`	, base in the index

field PSEUDOCOUNT #

PSEUDOCOUNT

加一平滑所引入的伪计数

field columnObserved #

columnObserved

每一列之上实际观测到的碱基数量，N 等非标准字符不计入