screenMatch {cellHTS} | R Documentation |
Match the annotation of two cellHTS
objects in order to find the common
gene-perturbing reagents
screenMatch(screens, ids)
screens |
a list of annotated cellHTS objects. |
ids |
a character vector of length two giving, for each cellHTS object, the name of the column of slot 'geneAnno' that should be used for the annotation IDs. See details. |
By default, if ids
is missing, the column GeneID
of the slot geneAnno
of each of the cellHTS
objects in screens
is taken for the annotation IDs when comparing the two data sets.
A list with two components:
p.overlap |
a vector giving the proportion of overlap in the screens' annotation. |
isInBoth |
a list of logical vectors, each of which with length equal to the product between nr. Well and nr. Plates in each screen, indicating whether the respective gene-perturbing reagent of that screen is also present in the other. |
Ligia Braz ligia@ebi.ac.uk
## Just for exemplification purposes, we consider the complete genome-wide screen "KcViab" ## and its first 3 plates ("KcViabSmall"): data(KcViab) data(KcViabSmall) screens <- list(KcViab, KcViabSmall) out <- screenMatch(screens) out$p.overlap sapply(out$isInBoth, sum) sapply(1:2, function(z) table(screens[[z]]$geneAnno$Plate[out$isInBoth[[z]]]))