Bed2Range
(Package: customProDB) :
Generate a GRanges objects from BED file.
Read BED file into a GRanges object. This function requires complete BED file. Go to https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for more information about BED format.
● Data Source:
BioConductor
● Keywords:
● Alias: Bed2Range
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InputVcf
(Package: customProDB) :
Generate a list of GRanges objects from a VCF file.
The InputVcf() function generates a list of GRanges object from a single VCF file.
● Data Source:
BioConductor
● Keywords:
● Alias: InputVcf
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JunctionType
(Package: customProDB) :
Annotates the junctions in a bed file.
For identified splice junctions from RNA-Seq, this function finds the junction types for each entry according to the given annotation. Six types of junctions are classified. find more details in the tutorial.
● Data Source:
BioConductor
● Keywords:
● Alias: JunctionType
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Multiple_VCF
(Package: customProDB) :
Generate shared variation dataset from multiple VCF files
Load multiple vcf files and output a GRange object with SNVs present in multiple samples.
● Data Source:
BioConductor
● Keywords:
● Alias: Multiple_VCF
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OutputNovelJun
(Package: customProDB) :
generate peptide FASTA file that contains novel junctions.
Three-frame translation of novel junctions. And remove those could be found in normal protein sequences. This function requires a genome built by BSgenome package.
● Data Source:
BioConductor
● Keywords:
● Alias: OutputNovelJun
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OutputVarproseq
(Package: customProDB) :
Output the variant(SNVs) protein sequences into FASTA format
Output the non-synonymous SNVs into FASTA file.
● Data Source:
BioConductor
● Keywords:
● Alias: OutputVarproseq
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OutputVarproseq_single
(Package: customProDB) :
Output the variant(SNVs) protein sequences into FASTA format
Output the non-synonymous SNVs into FASTA file, one SNV per sequence.
● Data Source:
BioConductor
● Keywords:
● Alias: OutputVarproseq_single
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Outputaberrant
(Package: customProDB) :
generate FASTA file containing short INDEL
Short insertion/deletion may lead to aberrant proteins in cells. We provide a function to generate FASTA file containing this kind of proteins.
● Data Source:
BioConductor
● Keywords:
● Alias: Outputaberrant
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Outputproseq
(Package: customProDB) :
output FASTA format file contains proteins that have expression level above the cutoff
Get the FASTA file of proteins that pass RPKM cutoff. the FASTA ID line contains protein ID, gene ID, HGNC symbol and description
● Data Source:
BioConductor
● Keywords:
● Alias: Outputproseq
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OutputsharedPro
(Package: customProDB) :
Output the sequences of proteins with high expressions in multiple samples.
Output a FASTA file containing shared proteins with expression above cutoff in multiple samples
● Data Source:
BioConductor
● Keywords:
● Alias: OutputsharedPro
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