seqminer-package |
Efficiently Read Sequencing Data (VCF format, METAL format) into R |
addJob |
Add a job to a workflow |
annotateGene |
Annotate a test variant |
annotatePlain |
Annotate a plain text file |
annotateVcf |
Annotate a VCF file |
createSingleChromosomeBCFIndex |
Create a single chromosome index |
createSingleChromosomeVCFIndex |
Create a single chromosome index |
download.annotation.resource |
Download annotation resources to a directory |
getCovPair |
Extract pair of positions by ranges |
getRefBase |
Annotate a test variant |
isDirWritable |
Test whether directory is writable |
isInRange |
Test whether a vector of positions are inside given ranges |
isTabixRange |
Check if the inputs are valid tabix range such as chr1:2-300 |
makeAnnotationParameter |
Construct a usable set of annotation parameters |
newJob |
Create a new job |
newWorkflow |
Create a new workflow |
openPlink |
Open binary PLINK files |
readBGENToListByGene |
Read information from BGEN file in a given range and return a list |
readBGENToListByRange |
Read information from BGEN file in a given range and return a list |
readBGENToMatrixByGene |
Read a gene from BGEN file and return a genotype matrix |
readBGENToMatrixByRange |
Read a gene from BGEN file and return a genotype matrix |
readPlinkToMatrixByIndex |
Read from binary PLINK file and return a genotype matrix |
readSingleChromosomeBCFToMatrixByRange |
Read a range from BCF file and return a genotype matrix |
readSingleChromosomeVCFToMatrixByRange |
Read a range from VCF file and return a genotype matrix |
readVCFToListByGene |
Read information from VCF file in a given range and return a list |
readVCFToListByRange |
Read information from VCF file in a given range and return a list |
readVCFToMatrixByGene |
Read a gene from VCF file and return a genotype matrix |
readVCFToMatrixByRange |
Read a gene from VCF file and return a genotype matrix |
rvmeta.readCovByRange |
Read covariance by range from METAL-format files. |
rvmeta.readDataByGene |
Read association statistics by gene from METAL-format files. Both score statistics and covariance statistics will be extracted. |
rvmeta.readDataByRange |
Read association statistics by range from METAL-format files. Both score statistics and covariance statistics will be extracted. |
rvmeta.readNullModel |
Read null model statistics |
rvmeta.readScoreByRange |
Read score test statistics by range from METAL-format files. |
rvmeta.readSkewByRange |
Read skew by range from METAL-format files. |
rvmeta.writeCovData |
Write covariance association statistics files. |
rvmeta.writeScoreData |
Write score-based association statistics files. |
seqminer |
Efficiently Read Sequencing Data (VCF format, METAL format) into R |
tabix.createIndex |
Create tabix index file, similar to running tabix in command line. |
tabix.createIndex.meta |
Create tabix index for bgzipped MetaScore/MetaCov file |
tabix.createIndex.vcf |
Create tabix index for bgzipped VCF file |
tabix.read |
Read tabix file, similar to running tabix in command line. |
tabix.read.header |
Read tabix file, similar to running tabix in command line. |
tabix.read.table |
Read tabix file, similar to running tabix in command line. |
validateAnnotationParameter |
Validate annotate parameter is valid |
verifyFilename |
validate the inVcf can be created, and outVcf can be write to. will stop if any error occurs |
writeWorkflow |
Export workflow to Makefile |
[.PlinkFile |
Read from binary PLINK file and return a genotype matrix |