deleteMatrixHavingID-methods: JASPAR database operations

Description Usage Arguments Value Examples

Description

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

Usage

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  ## 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

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  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 Sept. 12, 2021, 12:07 p.m.