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| ## Overview | ||
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| Running a PC-corrected project is an option only after you have already run a project in Genvisis. The PC-corrected project is a copy of the original project in which X and Y are transformed based on the nearest genotype cluster using a user-specified number of principal components. Genvisis recomputes LRR and BAF on the new X and Y values. | ||
| A PC-corrected project is a copy of your original Genvisis project in which X and Y are transformed based on the nearest genotype cluster using a user-specified number of principal components. Genvisis recomputes LRR and BAF on the new X and Y values. You cannot run a PC-corrected project without first running a project in Genvisis. | ||
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| ### Creates files: | ||
| * data/ | ||
| * batch.txt (if present in the parent project) | ||
| * import.ser | ||
| * linker.txt | ||
| * markerdetails.ser | ||
| * markers.ser | ||
| * pedigree.txt | ||
| * SampleData.txt | ||
| * DNA | ||
| * Batch (if a batch file was used) | ||
| * CLASS=Batch (if a batch file was used) | ||
| * CLASS=Sex | ||
| * CLASS=Estimated Sex;0=Unknown;1=Male;2=Female;3=Klinefelter;4=UPD Klinefelter;5=Mosaic Klinefelter;6=Triple X;7=Mosaic Triple X;8=Turner;9=Mosaic Turner | ||
| * Class=ImputedRace;1=White;2=African American;3=Hispanic;4=Asian | ||
| * % African | ||
| * % Asian | ||
| * % European | ||
| * mzTwinID | ||
| * Aneuploidy | ||
| * AnyTrisomy | ||
| * AnyLargeMosaicEvent | ||
| * numChrsWithEventGreaterThan4 | ||
| * NumberMosaicEventsDetected | ||
| * ProportionGenomeMosaic | ||
| * PCA/PCA\_GENVISIS/PCA\_GENVISISLRR\_SD | ||
| * PCA/PCA\_GENVISIS/PCA\_GENVISISGenotype\_callrate | ||
| * PCA/PCA\_GENVISIS/PCA\_GENVISISCLASS=Exclude | ||
| * samples.ser | ||
| * samples/ | ||
| * Empty. The first step of the PC-Corrected workflow Transpose Marker Files to Samples Files will populate this directory. | ||
| * scripts/ | ||
| * .slrm file | ||
| * .toml file | ||
| * Appears if Create script with steps to process corrected data and call CNVs? option is checked in the Create PC-Corrected Project step. | ||
| * transposed/ | ||
| * Marker dominant .mdRAF files with recalculated X, Y, LRR, and BAF values. | ||
| * #\_markersThatFailedCorrection.txt | ||
| * List of markers that could not be PC-corrected | ||
| * AB\_lookup\_parsed.dat | ||
| * .csv manifest (Illumina projects only) | ||
| * markerPositions.txt | ||
| When you run a PC-corrected project, Genvisis creates several files: | ||
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| - data/ | ||
| - batch.txt (if present in the parent project) | ||
| - import.ser | ||
| - linker.txt | ||
| - markerdetails.ser | ||
| - markers.ser | ||
| - pedigree.txt | ||
| - SampleData.txt | ||
| - DNA | ||
| - Batch (if a batch file was used) | ||
| - CLASS=Batch (if a batch file was used) | ||
| - CLASS=Sex | ||
| - CLASS=Estimated Sex;0=Unknown;1=Male;2=Female;3=Klinefelter;4=UPD Klinefelter;5=Mosaic Klinefelter;6=Triple X;7=Mosaic Triple X;8=Turner;9=Mosaic Turner | ||
| - Class=ImputedRace;1=White;2=African American;3=Hispanic;4=Asian | ||
| - % African | ||
| - % Asian | ||
| - % European | ||
| - mzTwinID | ||
| - Aneuploidy | ||
| - AnyTrisomy | ||
| - AnyLargeMosaicEvent | ||
| - numChrsWithEventGreaterThan4 | ||
| - NumberMosaicEventsDetected | ||
| - ProportionGenomeMosaic | ||
| - PCA/PCA\_GENVISIS/PCA\_GENVISISLRR\_SD | ||
| - PCA/PCA\_GENVISIS/PCA\_GENVISISGenotype\_callrate | ||
| - PCA/PCA\_GENVISIS/PCA\_GENVISISCLASS=Exclude | ||
| - samples.ser | ||
| - samples/ | ||
| - Initially this directory will be empty; the first step of the PC-Corrected workflow (**Transpose Marker Files to Samples Files**) will populate this directory | ||
| - scripts/ | ||
| - .slrm file | ||
| - .toml file | ||
| - Appears if **Create PC-Corrected Project step > Create script with steps to process corrected data and call CNVs?** is checked | ||
| - transposed/ | ||
| - marker-dominant **.mdRAF** files with recalculated X, Y, LRR, and BAF values | ||
| - #\_markersThatFailedCorrection.txt | ||
| - List of markers that could not be PC-corrected | ||
| - AB\_lookup\_parsed.dat | ||
| - **.csv** manifest (Illumina projects only) | ||
| - **markerPositions.txt** |