importRdata: Create SwitchAnalyzeRlist From Standard R Objects

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/import_data.R

Description

A general-purpose interface to constructing a switchAnalyzeRlist. The data needed for this function are

Please note that

Usage

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importRdata(
    ### Core arguments
    isoformCountMatrix,
    isoformRepExpression = NULL,
    designMatrix,
    isoformExonAnnoation,
    isoformNtFasta = NULL,
    comparisonsToMake = NULL,

    ### Advanced arguments
    addAnnotatedORFs = TRUE,
    onlyConsiderFullORF = FALSE,
    removeNonConvensionalChr = FALSE,
    ignoreAfterBar = TRUE,
    ignoreAfterSpace = TRUE,
    ignoreAfterPeriod = FALSE,
    removeTECgenes = TRUE,
    PTCDistance = 50,
    foldChangePseudoCount = 0.01,
    addIFmatrix = TRUE,
    fixStringTieAnnotationProblem = TRUE,
    fixStringTieViaOverlapInMultiGenes = TRUE,
    fixStringTieMinOverlapSize = 50,
    fixStringTieMinOverlapFrac = 0.2,
    fixStringTieMinOverlapLog2RatioToContender = 0.65,
    estimateDifferentialGeneRange = TRUE,
    showProgress = TRUE,
    quiet = FALSE
)

Arguments

isoformCountMatrix

A data.frame with unfiltered independent biological (aka not technical) replicate isoform (estimated) fragment counts (see FAQ in vignette for more details) with genes as rows and samples as columns. Must have a column called 'isoform_id' with the isoform_id that matches the isoform_id column in isoformExonAnnoation. The name of the columns must match the sample names in the designMatrix argument and contain the estimated counts.

isoformRepExpression

Optional but highly recommended: A data.frame with unfiltered normalized independent biological (aka not technical) replicate isoform expression (see FAQ in vignette for more details). Ideal for supplying quantification measured in Transcripts Per Million (TxPM) or RPKM/FPKM. Must have a column called 'isoform_id' that matches the isoform_id column in isoformExonAnnoation. The name of the expression columns must match the sample names in the designMatrix argument. If not supplied RPKM values are calculated from the count matrix and used instead.

designMatrix

A data.frame with the information of which samples originate from which conditions. Must be a data.frame containing at least these two columns:

  • Column 1: called 'sampleID'. This column contains the sample names and must match the column names used in isoformRepExpression.

  • Column 2: called 'condition'. This column indicates with a string which conditions the sample originate from. If sample 1-3 originate form the same condition they should all have the same string (for example 'ctrl', in this column).

Additional columns can be used to describe other co-factors such as batch effects or patient ids (for paired sample analysis). For more information see discussion of cofactors in vignette.

isoformExonAnnoation

Can either be:

  • 1: A string indicating the full path to the (gziped or unpacked) GTF file with the annotation of the isoforms quantified. If you are using a refrence-only workflow (tools such as Kallisto/Salmon/RSEM etc) this argument should point to the refrence database GTF corresponding to the fasta file that you used to build the refrence index. If you use a guided/de-novo transcriptome assembly approach (tools like StringTie and Cufflinks) this argument should point to the GTF file created at the "merge" stage of the workflow. Please refere to the "What Quantification Tool(s) Should I Use" section of the vignette for a more detailed description of the two different workflows. An example could be "myAnnotation/myGenome/isoformsQuantified.gtf")

  • 2: A string indicating the full path to the (gziped or unpacked) RefSeq GFF file which have been quantified. If supplied the exon structure and isoform annotation will be obtained from the GFF file. Please note only GFF files from RefSeq downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/ are supported (see database FAQ in vignette for more info). An example could be "RefSeq/isoformsQuantified.gff")

  • 3: A GRange object (see ?GRanges) containing one entry per exon per isoform with the genomic coordinates of that exon. This GRange should furthermore contain two meta data columns called 'isoform_id' and 'gene_id' indicating both which isoform the exon belongs to as well as which gene the isoform belongs to. The 'isoform_id' column must match the isoform ids used in the 'isoform_id' column of the isoformRepExpression data.frame. If possible we suggest that a third columns called 'gene_name' with the corresponding gene names/symbols is also added. If not supplied gene_name will be annotated as missing (NA).

isoformNtFasta

A (vector of) text string(s) providing the path(s) to the a fasta file containing the nucleotide sequence of all isoforms quantified. This is useful for: 1) people working with non-model organisms where extracting the sequence from a BSgenome might require extra work. 2) workflow speed-up for people who already have the fasta file (which most people running Salmon, Kallisto or RSEM for the quantification have as that is used to build the index). The file(s) will automatically be subsetted to the isoforms found in the expression matrix so additional sequences (such as decoys) does not need to be manually removed. Please note this different from a fasta file with the sequences of the entire genome.

comparisonsToMake

A data.frame with two columns indicating which pairwise comparisons the switchAnalyzeRlist created should contain. The two columns, called 'condition_1' and 'condition_2' indicate which conditions should be compared and the strings indicated here must match the strings in the designMatrix$condition column. If not supplied all pairwise (unique non directional) comparisons of the conditions given in designMatrix$condition are created. If only a subset of the supplied data is used in the comparisons the Un-used data is automatically removed.

addAnnotatedORFs

Only used if a GTF file is supplied to isoformExonAnnoation. A logic indicating whether the ORF from the GTF should be added to the switchAnalyzeRlist. This ORF is defined as the regions annotated as 'CDS' in the 'type' column (column 3). Default is TRUE.

onlyConsiderFullORF

A logic indicating whether the ORFs added should only be added if they are fully annotated. Here fully annotated is defined as those that both have a annotated 'start_codon' codon in the 'type' column (column 3). This argument exists because these CDS regions are highly problematic and does not resemble true ORFs as >50% of CDS without a stop_codon annotated contain multiple stop codons (see Vitting-Seerup et al 2017 - supplementary materials). This argument is only considered if addAnnotatedORFs=TRUE. Default is FALSE.

removeNonConvensionalChr

A logic indicating whether non-conventional chromosomes, here defined as chromosome names containing either a '_' or a period ('.'). These regions are typically used to annotate regions that cannot be associated to a specific region (such as the human 'chr1_gl000191_random') or regions quite different due to different haplotypes (e.g. the 'chr6_cox_hap2'). Default is FALSE.

ignoreAfterBar

A logic indicating whether to subset the isoform ids by ignoring everything after the first bar ("|"). Useful for analysis of GENCODE data. Default is TRUE.

ignoreAfterSpace

A logic indicating whether to subset the isoform ids by ignoring everything after the first space (" "). Useful for analysis of gffutils generated GTF files. Default is TRUE.

ignoreAfterPeriod

A logic indicating whether to subset the gene/isoform is by ignoring everything after the first period ("."). Should be used with care. Default is FALSE.

removeTECgenes

A logic indicating whether to remove genes marked as "To be Experimentally Confirmed" (if annotation is available). The default is TRUE aka to remove them which is in line with Gencode recommendations (TEC are not in Gencode annotations). For more info about TEC see https://www.gencodegenes.org/pages/biotypes.html.

PTCDistance

Only used if a GTF file is supplied to isoformExonAnnoation and addAnnotatedORFs=TRUE. A numeric giving the premature termination codon-distance: The minimum distance from the annotated STOP to the final exon-exon junction, for a transcript to be marked as NMD-sensitive. Default is 50

foldChangePseudoCount

A numeric indicating the pseudocount added to each of the average expression values before the log2 fold change is calculated. Done to prevent log2 fold changes of Inf or -Inf. Default is 0.01

addIFmatrix

A logic indicating whether to add the Isoform Fraction replicate matrix (if TRUE) or not (if FALSE). Keeping it will make testing with isoformSwitchTestDEXSeq faster but will also make the switchAnalyzeRlist larger - so it is a trade off for speed vs memory. For most experimental setups we expect that keeping it will be the better solution. Default is TRUE.

fixStringTieAnnotationProblem

A logic indicating whether to try and fix the following two annoation problems.

  • 1: Fix the problem where novel isoforms are not assigned to a refrence gene. This is done by assigning the gene_name of the parrent gene_id, but only when the gene_id is associated with a single gene_name.

  • 2: Fix the problem where multiple genes (as indicated by refrence gene_ids) are merged into a single gene_id. This can only be done when all isoforms are assigned a gene_name. The gene_id is simply split into multiple gene_ids via the gene_names. Genes with this problem, which could not be fixed, are removed since such constallations might result in untrustworthy switches (where the isoforms are acutally from different genes).

  • 3: Fix the problem where all genes containing novel isoforms are assigned a StringTie gene_id instead of their original id. This is done by assigning the gene_name of the parrent gene_id, but only when the gene_id is associated with a single gene_name.

Default is TRUE.

fixStringTieViaOverlapInMultiGenes

A logic indicating whether the IsoformSwitchAnalyzeR should also try to assign gene_names to novel isoforms within gene_ids with multiple gene_names associated. This is done by comparing the genomic overlap of exons in novel isoforms to exons in known isoforms. This is only done if all of the fixStringTieViaOverlap* cutoffs are met and fixStringTieAnnotationProblem=TRUE. Default is TRUE.

fixStringTieMinOverlapSize

The minimum number of nucleotide a novel isoform must overlap with a known isoform for gene_name transfer. This argument modulates the process described in the fixStringTieViaOverlapInMultiGenes argument. Default is 50.

fixStringTieMinOverlapFrac

The minimum fraction of a novel isoform must overlap with a known isoform for gene_name transfer. This argument modulates the process described in the fixStringTieViaOverlapInMultiGenes argument. Default is 0.2.

fixStringTieMinOverlapLog2RatioToContender

A log2 ratio which describes how much larger the overlap between a novel isoform and a known isoform must be for gene_name transfer in cases where overlap with known isoforms from multiple gene_names occure. This is the most important argument of deciding what to do with isoform overlapping multiple genes. If increased only more certain cases are assigned at the cost of more isoforms not being assigned. If decrease more isoforms are assigned but the certainty is lower. The default is 0.65 (corresponding to approx 1.57 fold) which according to our test data is the best a balance between strict and lenient.

estimateDifferentialGeneRange

A logic indicating whether to make a very quick estimate of the number of genes with differential isoform usage. Please note this number should be taken as a pilot and cannot be trusted. It merely servers to indcate what could be expected if the data is analyzed with the rest of the IsoformSwitchAnalyzeR. See details for more information. Default is TRUE.

showProgress

A logic indicating whether to make a progress bar (if TRUE) or not (if FALSE). Default is FALSE.

quiet

A logic indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE

Details

For each gene in each replicate sample the expression of all isoforms belonging to that gene (as annotated in isoformExonAnnoation) are summed to get the gene expression. It is therefore very important that the isoformRepExpression is unfiltered. For each gene/isoform in each condition (as indicate by designMatrix) the mean and standard error (of mean (measurement), s.e.m) are calculated. Since all samples are considered it is very important the isoformRepExpression does not contain technical replicates. The comparison indicated comparisonsToMake (or all pairwise if not supplied) is then constructed and the mean gene and isoform expression values are then used to calculate log2 fold changes (using foldChangePseudoCount) and Isoform Fraction (IF) values. The whole analysis is then wrapped in a SwitchAnalyzeRlist.

Changes in isoform usage are measure as the difference in isoform fraction (dIF) values, where isoform fraction (IF) values are calculated as <isoform_exp> / <gene_exp>.

The guestimate produced by setting estimateDifferentialGeneRange = TRUE is created by subsetting a lot on data (both on samples, conditions and genes) and running a fast but unreliable DTU method. The resulting number is then multiplied by a factor to caclulate back what would be expected by running the IsoformSwitchAnalyzeR pipeline. It should go without saying due to all these factors the acutal guestimate is just that - and estimate which cannot be trusted but merely indicate the expected range. It is to be expected the acutal results from running the IsoformSwitchAnalyzeR pipeline differs from the guestimate in which case the guestimate should not be trusted.

Value

A SwitchAnalyzeRlist containing the data supplied stored into the SwitchAnalyzeRlist format (created by createSwitchAnalyzeRlist()). For details about the format see details of createSwitchAnalyzeRlist.

If a GTF file was supplied to isoformExonAnnoation and addAnnotatedORFs=TRUE a data.frame containing the details of the ORF analysis have been added to the switchAnalyzeRlist under the name 'orfAnalysis'. The data.frame added have one row pr isoform and contains 11 columns:

NA means no information was available aka no ORF (passing the minORFlength filter) was found.

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
importIsoformExpression
preFilter

Examples

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### Please note
# 1) The way of importing files in the following example with
#       "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is
#       specialized way of accessing the example data in the IsoformSwitchAnalyzeR package
#       and not something you need to do - just supply the string e.g.
#       isoformExonAnnoation = "myAnnotation/isoformsQuantified.gtf" to the functions
# 2) importRdata directly supports import of a GTF file - just supply the
#       path (e.g. "myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument

### Import quantifications
salmonQuant <- importIsoformExpression(system.file("extdata/", package="IsoformSwitchAnalyzeR"))

### Make design matrix
myDesign <- data.frame(
    sampleID = colnames(salmonQuant$abundance)[-1],
    condition = gsub('_.*', '', colnames(salmonQuant$abundance)[-1])
)

### Create switchAnalyzeRlist
aSwitchList <- importRdata(
    isoformCountMatrix   = salmonQuant$counts,
    isoformRepExpression = salmonQuant$abundance,
    designMatrix         = myDesign,
    isoformExonAnnoation = system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR"),
    isoformNtFasta       = system.file("extdata/example_isoform_nt.fasta.gz", package="IsoformSwitchAnalyzeR")
)
aSwitchList

kvittingseerup/IsoformSwitchAnalyzeR documentation built on May 12, 2021, 12:25 p.m.