deleteMatrixHavingID-methods: JASPAR database operations

In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

JASPAR database operations

Description

The functions to initialize, store matrix or delete matrix in JASPAR database.

Usage

  ## S4 method for signature 'character'
deleteMatrixHavingID(x, IDs)
  ## S4 method for signature 'SQLiteConnection'
deleteMatrixHavingID(x, IDs)
  ## S4 method for signature 'JASPAR2014'
deleteMatrixHavingID(x, IDs)
  ## S4 method for signature 'character,PFMatrixList'
storeMatrix(x, pfmList)
  ## S4 method for signature 'SQLiteConnection,PFMatrixList'
storeMatrix(x, pfmList)
  ## S4 method for signature 'JASPAR2014,PFMatrixList'
storeMatrix(x, pfmList)
  ## S4 method for signature 'character,PFMatrix'
storeMatrix(x, pfmList)
  ## S4 method for signature 'SQLiteConnection,PFMatrix'
storeMatrix(x, pfmList)
  ## S4 method for signature 'JASPAR2014,PFMatrix'
storeMatrix(x, pfmList)
  ## S4 method for signature 'SQLiteConnection'
initializeJASPARDB(x, version=c("2014", "2016", "2018", "2020", "2022"))
  ## S4 method for signature 'character'
initializeJASPARDB(x, version=c("2014", "2016", "2018", "2020", "2022"))
  ## S4 method for signature 'JASPAR2014'
initializeJASPARDB(x, version)
  ## S4 method for signature 'JASPAR2016'
initializeJASPARDB(x, version)
  ## S4 method for signature 'JASPAR2018'
initializeJASPARDB(x, version)
  ## S4 method for signature 'JASPAR2020'
initializeJASPARDB(x, version)

Arguments

x	A character vector of length 1 for the path of JASPAR SQLite file, or a SQLiteConnection object.
IDs	JASPAR stable IDs.
pfmList	The PFMatrixList object, or pfm object.
version	Which version of JASPAR to create. So far, it supports 2014, 2016 and 2018.

Value

If the operation works, a "success" will be returned.

Examples

  initializeJASPARDB("jaspar.sqlite", version="2014")
  data("MA0043")
  storeMatrix("jaspar.sqlite", MA0043)
  deleteMatrixHavingID("jaspar.sqlite","MA0043.1")
  file.remove("jaspar.sqlite")

ge11232002/TFBSTools documentation built on Dec. 26, 2024, 12:38 a.m.