preFilter: Filtering of a switchAnalyzeRlist

In kvittingseerup/IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Filtering of a switchAnalyzeRlist

Description

This function removes genes/isoforms from a switchAnalyzeRlist with the aim of allowing faster processing time as well as more trustworthy results.

Usage

preFilter <- function(
    switchAnalyzeRlist,
    isoCount = 10,
    min.Count.prop = 0.7,
    IFcutoff = 0.1,
    min.IF.prop = 0.5,
    acceptedGeneBiotype = NULL,
    acceptedIsoformClassCode = NULL,
    removeSingleIsoformGenes = TRUE,
    reduceToSwitchingGenes = FALSE,
    reduceFurtherToGenesWithConsequencePotential = FALSE,
    onlySigIsoforms = FALSE,
    keepIsoformInAllConditions = FALSE,
    alpha = 0.05,
    dIFcutoff = 0.1
)

Arguments

switchAnalyzeRlist	A switchAnalyzeRlist object.
isoCount	The cutoff specifies the minimum isoform counts level for a certain proportion of samples in each comparison. Setting this to NULL disables the filter (not recommended). The default is 10.
min.Count.prop	The cutoff specifies the minimum proportion of samples in each comparison that must express isoforms at certain counts. It should be used with isoCount. Setting this to NULL disables the filter (not recommended). The default value is 0.7.
IFcutoff	The cutoff specifies the minimum isoform usage (measured as Isoform Fraction, see details) for a certain proportion of samples in each comparison. Setting this to NULL disables the filter (not recommended). The default is 0.1.
min.IF.prop	The cutoff specifies the minimum proportion of samples in each comparison with more than certain isoform usage. It should be used with IFcutoff. Setting this to NULL disables the filter (not recommended). The default value is 0.5.
acceptedGeneBiotype	A vector of strings indicating which gene biotypes (data typically obtained from GTF files). Can be any biotype annotated, the most common being: "protein_coding", "lincRNA" and "antisense". Default is NULL.
acceptedIsoformClassCode	A vector of strings indicating which cufflinks class codes are accepted. Can only be used if data origins from cufflinks. For an updated list with full description see the bottom of this website: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/#tracking-transfrags-through-multiple-samples-outprefixtracking. Set to NULL to disable. Default is NULL.
removeSingleIsoformGenes	A logic indicating whether to only keep genes containing more than one isoform (in any comparison, after the other filters have been applied). Default is TRUE.
reduceToSwitchingGenes	A logic indicating whether the switchAnalyzeRlist should be reduced to the genes which contains significant switching (as indicated by the alpha and dIFcutoff parameters). Enabling this will make the downstream analysis a lot faster since fewer genes needs to be analyzed. Requires a test of isoform switches have been performed. Default is FALSE.
reduceFurtherToGenesWithConsequencePotential	A logic indicating whether the switchAnalyzeRlist should be reduced to the genes which have the potential to find isoform switches with predicted consequences. This argument is a more strict version of reduceToSwitchingGenes as it not only requires that at least one isoform is significantly differential used (as indicated by the alpha and dIFcutoff parameters) but also that there is an isoform with the opposite effect size (e.g. used less if the first isoform is used more). The minimum effect size of the opposing isoform usage is also controlled by dIFcutoff. The existence of such an opposing isoform means a switch pair can be formed. It is these pairs that can be analyzed for functional consequences further downstream in the IsoformSwitchAnalyzeR workflow. Enabling this will make the downstream analysis a even faster (than just using reduceToSwitchingGenes) since fewer genes needs to be analyzed. Requires that reduceToSwitchingGenes=TRUE to have any effect. Default is FALSE.
onlySigIsoforms	A logic indicating whether both isoforms the pairs considered if reduceFurtherToGenesWithConsequencePotential=TRUE should be significantly differential used (as indicated by the alpha and dIFcutoff parameters). Default is FALSE (aka only one of the isoforms in a pair should be significantly differential used).
keepIsoformInAllConditions	A logic indicating whether the an isoform should be kept in all comparisons even if it is only passes the filters in one comparison. Default is FALSE.
alpha	The cutoff which the FDR correct p-values must be smaller than for calling significant switches. Only considered if reduceToSwitchingGenes=TRUE. Default is 0.05.
dIFcutoff	The cutoff which the changes in (absolute) isoform usage must be larger than before an isoform is considered switching. This cutoff can remove cases where isoforms with (very) low dIF values are deemed significant and thereby included in the downstream analysis. This cutoff is analogous to having a cutoff on log2 fold change in a normal differential expression analysis of genes to ensure the genes have a certain effect size. Only considered if reduceToSwitchingGenes=TRUE. Default is 0.1 (10%).
quiet	A logic indicating whether to avoid printing progress messages. Default is FALSE

Details

The filtering process starts by retaining isoforms with at least isoCount reads and IFcutoff usage in a significant proportion of samples within comparisons. This proportion addresses variable and unbalanced (10 vs 3) sample sizes in the comparisons. Next, the data is filtered for isoform classes, and finally, for single-isoform genes.

Please note that for the exon entry as well as any replicate matrix entry (counts, abundances or isoform fractions) all isoforms from genes where at least one isoform passed the filters are kept.

Value

A switchAnalyzeRlist object where the genes and isoforms not passing the filters have been removed (from all annotated entries)

Author(s)

Kristoffer Vitting-Seerup

References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

See Also

createSwitchAnalyzeRlist
importCufflinksFiles
importRdata

Examples

data("exampleSwitchList")
exampleSwitchListFiltered <- preFilter(
    exampleSwitchList,
    isoCount = 10,
    min.Count.prop = 0.7,
    IFcutoff = 0.1,
    min.IF.prop = 0.5,
    removeSingleIsoformGenes = TRUE
)

kvittingseerup/IsoformSwitchAnalyzeR documentation built on June 28, 2024, 5:41 p.m.