NxtSE-class: The NxtSE class

In alexchwong/NxtIRFcore: Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

The NxtSE class

Description

The NxtSE class inherits from the SummarizedExperiment class and is constructed from MakeSE. NxtSE extends SummarizedExperiment by housing additional assays pertaining to IR and splice junction counts.

Usage

NxtSE(...)

## S4 method for signature 'NxtSE'
up_inc(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
down_inc(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
up_exc(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
down_exc(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
covfile(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
sampleQC(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
ref(x, withDimnames = TRUE, ...)

## S4 method for signature 'NxtSE'
realize_NxtSE(x, withDimnames = TRUE, ...)

## S4 replacement method for signature 'NxtSE'
up_inc(x, withDimnames = TRUE) <- value

## S4 replacement method for signature 'NxtSE'
down_inc(x, withDimnames = TRUE) <- value

## S4 replacement method for signature 'NxtSE'
up_exc(x, withDimnames = TRUE) <- value

## S4 replacement method for signature 'NxtSE'
down_exc(x, withDimnames = TRUE) <- value

## S4 replacement method for signature 'NxtSE'
covfile(x, withDimnames = TRUE) <- value

## S4 replacement method for signature 'NxtSE'
sampleQC(x, withDimnames = TRUE) <- value

## S4 method for signature 'NxtSE,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

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

## S4 method for signature 'NxtSE'
cbind(..., deparse.level = 1)

## S4 method for signature 'NxtSE'
rbind(..., deparse.level = 1)

Arguments

...	In NxtSE(), additional arguments to be passed onto SummarizedExperiment()
x	A NxtSE object
withDimnames	(default TRUE) Whether exported assays should be supplied with row and column names of the NxtSE object. See SummarizedExperiment
value	The value to replace. Must be a matrix for the up_inc<-, down_inc<-, up_exc<- and down_exc<- replacers, and a character vector for covfile<-
i, j	Row and column subscripts to subset a NxtSE object.
drop	A logical(1), ignored by these methods.
deparse.level	See base::cbind for a description of this argument.

Value

See Functions section (below) for details

Functions

• NxtSE: Constructor function for NxtSE; akin to SummarizedExperiment(...)

• up_inc,NxtSE-method: Gets upstream included events (SE/MXE), or upstream exon-intron spanning reads (IR)

• down_inc,NxtSE-method: Gets downstream included events (SE/MXE), or downstream exon-intron spanning reads (IR)

• up_exc,NxtSE-method: Gets upstream excluded events (MXE only)

• down_exc,NxtSE-method: Gets downstream excluded events (MXE only)

• covfile,NxtSE-method: Gets a named vector with the paths to the corresponding COV files

• sampleQC,NxtSE-method: Gets a data frame with the QC parameters of the samples

• ref,NxtSE-method: Retrieves a list of annotation data associated with this NxtSE object; primarily used in Plot_Coverage()

• realize_NxtSE,NxtSE-method: Converts all DelayedMatrix assays as matrices (i.e. performs all delayed calculation and loads resulting object to RAM)

• up_inc<-,NxtSE-method: Sets upstream included events (SE/MXE), or upstream exon-intron spanning reads (IR)

• down_inc<-,NxtSE-method: Sets downstream included events (SE/MXE), or downstream exon-intron spanning reads (IR)

• up_exc<-,NxtSE-method: Sets upstream excluded events (MXE only)

• down_exc<-,NxtSE-method: Sets downstream excluded events (MXE only)

• covfile<-,NxtSE-method: Sets the paths to the corresponding COV files

• sampleQC<-,NxtSE-method: Sets the values in the data frame containing sample QC

• [,NxtSE,ANY,ANY,ANY-method: Subsets a NxtSE object

• [<-,NxtSE,ANY,ANY,NxtSE-method: Sets a subsetted NxtSE object

• cbind,NxtSE-method: Combines two NxtSE objects (by samples - columns)

• rbind,NxtSE-method: Combines two NxtSE objects (by AS/IR events - rows)

Examples

# Run the full pipeline to generate a NxtSE object:

BuildReference(
    reference_path = file.path(tempdir(), "Reference"),
    fasta = chrZ_genome(), 
    gtf = chrZ_gtf()
)

bams <- NxtIRF_example_bams()
IRFinder(bams$path, bams$sample,
  reference_path = file.path(tempdir(), "Reference"),
  output_path = file.path(tempdir(), "IRFinder_output")
)

expr <- Find_IRFinder_Output(file.path(tempdir(), "IRFinder_output"))
CollateData(expr, 
  reference_path = file.path(tempdir(), "Reference"),
  output_path = file.path(tempdir(), "NxtIRF_output")
)

se <- MakeSE(collate_path = file.path(tempdir(), "NxtIRF_output"))

# Coerce NxtSE -> SummarizedExperiment
se_raw <- as(se, "SummarizedExperiment")

# Coerce SummarizedExperiment -> NxtSE
se_NxtSE <- as(se_raw, "NxtSE")
identical(se, se_NxtSE) # Returns TRUE

# Get Junction reads of SE / MXE and spans-reads of IR events
up_inc(se)
down_inc(se)
up_exc(se)
down_exc(se)

# Get list of available coverage files
covfile(se)

# Get sample QC information
sampleQC(se)

# Get resource NxtIRF data (used internally for Plot_Coverage())
cov_data <- ref(se)
names(cov_data)

# Subset functions
se_by_samples <- se[,1:3]
se_by_events <- se[1:10,]
se_by_rowData <- subset(se, EventType == "IR")

# Cbind (bind event_identical NxtSE by samples)
se_by_samples_1 <- se[,1:3]
se_by_samples_2 <- se[,4:6]
se_cbind <- cbind(se_by_samples_1, se_by_samples_2)
identical(se, se_cbind) # should return TRUE

# Rbind (bind sample_identical NxtSE by events)
se_IR <- subset(se, EventType == "IR")
se_SE <- subset(se, EventType == "SE")
se_IRSE <- rbind(se_IR, se_SE)
identical(se_IRSE, subset(se, EventType %in% c("IR", "SE"))) # TRUE

# Convert HDF5-based NxtSE to in-memory se
# MakeSE() creates a HDF5-based NxtSE object where all assay data is stored
# as an h5 file instead of in-memory. All operations are performed as
# delayed operations as per DelayedArray package.
# To realize the NxtSE object as an in-memory object, use:

se_real <- realize_NxtSE(se)
identical(se, se_real) # should return FALSE

# To check the difference, run:
class(up_inc(se))
class(up_inc(se_real))

alexchwong/NxtIRFcore documentation built on Oct. 31, 2022, 9:14 a.m.