getMissingGenotypes {qfa} | R Documentation |
For a given list of QFA numbers, finds all of the genotypes which we can classify as being missing in the first stage of each of the SGAs that preceded genome-wide QFA. We can assume that genotypes which are missing in the first stage of an SGA (where stains are not under marker-specific selection) are simply missing from the library (rather than synthetic lethal interaction with background mutation for example). Cultures with a specific genotype are classified as being missing if their fitness is less than thresfrac times the median fitness of all genotypes observed in that screen.
getMissingGenotypes(QFAs,threshfrac,mer)
QFAs |
List of QFA numbers to examine. |
threshfrac |
Genotypes whose median fitness is less than thresfrac times the genome-wide median will be classified as dead. |
mer |
Data frame representation of Lydall lab database file (as returned by readMer). |
Subset of rows from fitness reports containing information about genotypes classified as missing. ORF column contains systematic gene names. Gene column contains standard gene names.