extract-methods: Extract or replace parts of an object

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Extract or replace parts of an object

Description

Operators Giotto S4 internal data.tables to extract or replace parts.

Usage

## S4 method for signature 'coordDataDT'
x$name

## S4 replacement method for signature 'coordDataDT'
x$name <- value

## S4 method for signature 'metaData'
x$name

## S4 replacement method for signature 'metaData'
x$name <- value

## S4 method for signature 'coordDataDT,missing,ANY,missing'
x[i, j]

## S4 method for signature 'coordDataDT,ANY,missing,missing'
x[i, j]

## S4 method for signature 'coordDataDT,ANY,ANY,missing'
x[i, j]

## S4 method for signature 'coordDataDT,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'coordDataDT,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'metaData,missing,ANY,missing'
x[i, j]

## S4 method for signature 'metaData,ANY,missing,missing'
x[i, j]

## S4 method for signature 'metaData,ANY,ANY,missing'
x[i, j]

## S4 method for signature 'metaData,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'metaData,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'dimObj,ANY,ANY,missing'
x[i, j]

## S4 method for signature 'dimObj,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'dimObj,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'exprData,missing,ANY,missing'
x[i, j]

## S4 method for signature 'exprData,ANY,missing,missing'
x[i, j]

## S4 method for signature 'exprData,ANY,ANY,missing'
x[i, j]

## S4 method for signature 'exprData,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'exprData,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'spatNetData,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'spatNetData,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'nnData,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'nnData,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'enrData,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'enrData,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'spatGridData,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'spatGridData,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'giottoPoints,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'giottoPoints,missing,missing,ANY'
x[i, j] <- value

## S4 method for signature 'giottoPolygon,missing,missing,missing'
x[i, j]

## S4 replacement method for signature 'giottoPolygon,missing,missing,ANY'
x[i, j] <- value

Arguments

x	Giotto S4 object to extract columns from
name	A literal character string (possibly backtick quoted).
value	value(s) to set This is normally matched to the colnames of the data.table object within the S4.
i, j	indices specifying elements to extract or replace. Indices are numeric or character vectors or empty

`$` methods

Select by colname from giotto S4 data.table coordinates slot.

Select by colname from giotto S4 data.table metaDT slot.

`$<-` methods

Set values by colname into giotto S4 data.table coordinates slot. Works via data.table methods

Set values by colname into giotto S4 data.table metaDT slot. Works via data.table methods

`[` methods

Select rows (i) and cols (j) from giotto S4 coordinates slot

Return coordinates slot data.table from giotto S4

Select rows (i) and cols (j) from giotto S4 metaDT slot

Return metaDT slot data.table from giotto S4

Return coordinates slot matrix from giotto S4 dimObj

Select rows (i) and cols (j) from giotto S4 exprMat slot

Return exprMat slot Matrix object from giotto S4

Return spatNetData slot network data.table object from giotto S4

Return nnData slot igraph object from giotto S4

Return enrData slot enrichment data.table object from giotto S4

Return spatGridData slot data.table object from giotto S4

Return giottoPoints spatVector slot

Return giottoPolygon spatVector slot

`[<-` methods

Assign to coordinates slot in giotto S4

Assign to metaDT slot in giotto S4

Assign to coordinates slot in giotto S4 dimObj

Assign to exprMat slot in giotto S4

Assign to networkDT slot in giotto S4

Assign to igraph slot in giotto S4

Assign to enrichDT slot in giotto S4

Assign to gridDT slot in giotto S4

Assign to spatVector slot in giotto S4

Assign to spatVector slot in giottoPolygon

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.