changedXyChr | Split chromosome X into pseudoautosomal region and... |
chrWiseSplit | Split genome-wide genotyping data into separate files by... |
chunk4eachChr | Chunk each chromosome into multiple segments |
filterImputeData | Filter genetic variants |
formatConvertGtool | Convert IMPUTE2 format files into PLINK format |
imputedByImpute2 | Impute genotypes using IMPUTE2 |
mergeImputeData | Merge chunk-wise PLINK files |
plotPCA4plink | Population outlier detection via PCA |
prepareChipAnnoFile4affymetrix | prepare Affymetrix chip annotation file |
prepareChipAnnoFile4Illumina | prepare Illumina chip annotation file |
prePhasingByShapeit | Prephasing genotypes using SHAPEIT |
removedDoubleProbes | Remove duplicated probes or SNPs |
removedExclProbe | Remove probes or SNPs |
removedInstFhet | Remove subjects with great autosomal heterozygosity deviation |
removedInstMiss | Remove subjects with missing values |
removedMaleHetX | Remove male subjects with haploid heterozygous SNPs |
removedMonoSnp | Remove monomorphic SNPs |
removedParentIdsMiss | Reset paternal and maternal codes |
removedSnpFemaleChrXhweAll | Hardy weinberg equilibrium test for chromosome X SNPs in... |
removedSnpFemaleChrXhweControl | Hardy weinberg equilibrium test for chromosome X SNPs in... |
removedSnpFemaleChrXmiss | remove chromosome X SNPs in females |
removedSnpHetX | Remove heterozygous SNPs in haploid male chromosome X |
removedSnpHWEautoControl | Hardy weinberg equilibrium test for autosomal SNPs in... |
removedSnpMiss | Remove SNPs with missing values |
removedSnpMissDiff | Remove SNPs with difference in SNP missingness between cases... |
removedSnpMissPostImp | Remove SNPs after post imputation |
removedUnmapProbes | Remove unmapped probes or SNPs |
removeDupID | Remove duplicated sample IDs |
removedWrongAnceInst | Remove samples with improper ancestry |
removedYMtSnp | Remove SNPs on the chromosome Y and mitochondria |
removeNoGroupId | Remove samples without group information |
removeOutlierByPCs | Remove population outliers by principle components |
renamedSnpChr | Remaming chromosomes |
replaceGroupId | Replace group and geneder presentation into proper PLINK... |
setHeteroHaploMissing | Set haploid heterozygous SNPs as missing |
updatedSnpInfo | Update the probes or SNPs information |
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