Explaining example data of PepPrep package.
‘ExampleData.RData’ contains a data.frame called testtbl
(annotated single nucleotide variant (SNV)).
Columns in testtbl
:
Chr: Chromosom number
Start: Startposition
End: Endposition
Ref: Nucleotide in referencegenome
Obs: Observed Nucleotide
AAChange: Information from ANNOVAR it should look like NM_ID:c.Ref_Pos_Obs:p.RefAminoacid_Pos_MutAminoacid
Gene: Gene name
‘ExampleHomo_sapiens.GRCh37.70.pep.all.fa’
Contains the Ensembl protein ENSP00000361883 in FASTA format
‘ExampleHumanProt.fasta’
Two human protein sequneces from UniProt.
‘ExampleMouseProt.fasta’
Two mouse protein sequences from UniProt.
1 2 3 4 5 | testtbl <- system.file("extdata", "ExampleData.RData", package="PepPrep")
load(testtbl)
testtbl
attributes(testtbl)
lapply(testtbl,class)
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