Man pages for drmjc/blat
Import/Export functions for UCSC genome BLAT alignments
| alignment2psl | Take an alignment of targets to chromosome(s) where the... |
| blat-package | Methods to import, export and manipulate BLAT result data. |
| grow.bed | grow the intervals in a bed file |
| import.psl | Import a psl formatted alignment file of queries to targets |
| import.ucsc.bed | import a UCSC-format BED file |
| make.unique.psl | Convert a PSL alignment data.frame into a minimal 1:1... |
| midpoint.bed | Determine the midpoint of an interval |
| new.psl | Make a new empty psl table. |
| order.psl | determine the order of rows in a psl object, based on... |
| psl2bed | Convert a psl alignment from BLAT into a BED alignment. |
| psl2coordinates | convert psl file to UCSC-style coordinates |
| psl.besthit | obtain the best hit for each query |
| pslCalcMilliBad | internal function used to determing a psl alignment score. |
| pslIsProtein | is the psl alignment from a protein? |
| pslPercentIdentity | calculate the % identity of a psl alignment |
| pslPercentIdentity2 | calculate the % identity of a psl alignment V2 |
| pslPercentIdentity3 | calculate the % identity of a psl alignment V3 |
| pslScore | calculate the score from a psl alignment |
| sort.psl | sort a psl file such that each query is together, then by... |
| write.psl | Write a psl object out to a psl file. |
| write.ucsc.track | Write a psl object to a UCSC-style track |
