makeSE: Imports a collated dataset into the R session as an NxtSE...

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

Imports a collated dataset into the R session as an NxtSE object

Description

Creates a NxtSE object from the data (that was collated using collateData). This object is used for downstream differential analysis of IR and alternative splicing events using ASE-methods, data generation for visualization of scatter plots and heatmaps via make_plot_data methods, and coverage visualisation using plotCoverage

Usage

makeSE(
  collate_path,
  colData,
  RemoveOverlapping = TRUE,
  realize = FALSE,
  verbose = TRUE
)

Arguments

collate_path	(Required) The output path of collateData pointing to the collated data
colData	(Optional) A data frame containing the sample annotation information. The first column must contain the sample names. Omit colData to generate a NxtSE object of the whole dataset without any assigned annotations. Alternatively, if the names of only a subset of samples are given, then makeSE() will construct the NxtSE object based only on the samples given. The colData can be set later using colData
RemoveOverlapping	(default = TRUE) Whether to filter out overlapping IR events belonging to minor isoforms. See details.
realize	(default = FALSE) Whether to load all assay data into memory. See details
verbose	(default = TRUE) Whether loading messages are displayed

Details

makeSE retrieves the data collated by collateData, and initialises a NxtSE object. It references the required on-disk assay data using DelayedArrays, thereby utilising 'on-disk' memory to conserve memory usage.

For extremely large datasets, loading the entire data into memory may consume too much memory. In such cases, make a subset of the NxtSE object (e.g. subset by samples) before loading the data into memory (RAM) using realize_NxtSE. Alternatively supply a data frame to the colData parameter of the makeSE() function. Only samples listed in the first column of the colData data frame will be imported into the NxtSE object.

It should be noted that downstream applications of SpliceWiz, including ASE-methods, plotCoverage, are much faster if the NxtSE is realized. It is recommended to realize the NxtSE object before extensive usage.

If COV files assigned via collateData have been moved relative to the collate_path, the created NxtSE object will not be linked to any COV files and plotCoverage cannot be used. To reassign these files, a vector of file paths corresponding to all the COV files of the data set can be assigned using covfile(se) <- vector_of_cov_files. See the example below for details.

If RemoveOverlapping = TRUE, makeSE will remove introns that overlap other introns with higher junction read counts in the dataset. This means that SpliceWiz will assess a set of non-overlapping introns which belong to likely major isoforms, ensuring that overlapping IR events are not 'double-counted'.

NB: Since version 1.3.4, SpliceWiz has improved the algorithm of generating the set of non-overlapping introns (prior versions appear to generate sets of introns that still overlap). To use the prior algorithm for compatibility with prior analysis, set RemoveOverlapping = FALSE.

Value

A NxtSE object containing the compiled data in DelayedArrays (or as matrices if realize = TRUE), pointing to the assay data contained in the given collate_path

Examples

# The following code can be used to reproduce the NxtSE object
# that can be fetched with SpliceWiz_example_NxtSE()

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

bams <- SpliceWiz_example_bams()
processBAM(bams$path, bams$sample,
  reference_path = file.path(tempdir(), "Reference"),
  output_path = file.path(tempdir(), "SpliceWiz_Output")
)

expr <- findSpliceWizOutput(file.path(tempdir(), "SpliceWiz_Output"))
collateData(expr,
  reference_path = file.path(tempdir(), "Reference"),
  output_path = file.path(tempdir(), "Collated_output")
)

se <- makeSE(collate_path = file.path(tempdir(), "Collated_output"))

# "Realize" NxtSE object to load all H5 assays into memory:

se <- realize_NxtSE(se)

# If COV files have been removed since the last call to collateData()
# reassign them to the NxtSE object, for example:

covfile_path <- system.file("extdata", package = "SpliceWiz")
covfile_df <- findSamples(covfile_path, ".cov")

covfile(se) <- covfile_df$path

alexchwong/SpliceWiz documentation built on Oct. 15, 2024, 10:12 a.m.