View source: R/high_level_functions.R
isoformSwitchAnalysisPart1 | R Documentation |
This high-level function takes a pre-existing switchAnalyzeRlist as input (see importRdata
). Then part 1 of the workflow is performed. Specifically it is filtered to remove low expression, identifies significant isoform switches and ORF are predicted if not already annotated. Lastly the function extracts the nucleotide sequence and the ORF AA sequences of the isoforms involved in isoform switches. To enable external and internal sequence analysis these sequences are both saved to the computer (as fasta files) and added to the switchAnalyzeRlist.
This function is meant to be used as part 1 of the isoform switch analysis workflow, which can be followed by the second step via isoformSwitchAnalysisPart2
.
isoformSwitchAnalysisPart1(
### Core arguments
switchAnalyzeRlist,
### Annotation arguments
genomeObject = NULL,
pathToGTF = NULL,
### Output arguments
prepareForWebServers,
pathToOutput = getwd(),
outputSequences = TRUE,
### Other arguments
quiet = FALSE
)
switchAnalyzeRlist |
A |
genomeObject |
A |
pathToGTF |
A string indicating the full path to the (gziped or unpacked) GTF file which contains the the known annotation (aka from a official source) which was used to guided the transcript assembly (isoform deconvolution). |
prepareForWebServers |
A logical indicating whether the amino acid fasta files saved (if |
pathToOutput |
A path to the folder in which the plots should be made. Default is working directory ( getwd() ). |
outputSequences |
A logical indicating whether transcript nucleotide and amino acid sequences should be outputted to |
quiet |
A logical indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE |
This function performs the first part of a Isoform Analysis Workflow by
Remove low-expressed isoforms and single-isoform genes (see preFilter)
Identify isoform switches. This uses satuRn if there are more than 5 replicates in any condition and else DEXseq.
If no ORFs are annotated the isoforms are analyzed for open reading frames (ORFs, see analyzeORF)
The isoform nucleotide and ORF amino acid sequences are extracted and saved to fasta files as well as added to the switchAnalyzeRlist enabling external sequence analysis with CPAT, Pfam and SignalP (see vignette for more info).
if prepareForWebServers=TRUE
both the "removeLongAAseq" and "alsoSplitFastaFile" will be enabled in the extractSequence
function.
This function have two outputs. It returns a switchAnalyzeRlist
object where information about the isoform switch test, ORF prediction and nt and aa sequences have been added. Secondly (if outputSequences=TRUE
) the nucleotide and amino acid sequence of transcripts involved in switches are also save as fasta files enabling external sequence analysis.
Kristoffer Vitting-Seerup
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
preFilter
isoformSwitchTestDEXSeq
isoformSwitchTestSatuRn
analyzeORF
extractSequence
### load example data
data("exampleSwitchList")
### Subset for quick runtime
exampleSwitchList <- subsetSwitchAnalyzeRlist(
exampleSwitchList,
abs(exampleSwitchList$isoformFeatures$dIF) > 0.4
)
### Show summary
summary(exampleSwitchList)
### Run Part 1
exampleSwitchList <- isoformSwitchAnalysisPart1(
switchAnalyzeRlist=exampleSwitchList,
prepareForWebServers = FALSE,
outputSequences = FALSE # keeps the function from outputting the fasta files from this example
)
### Show summary
summary(exampleSwitchList)
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