Commit 210fec53 authored by aditya.bhagwat's avatar aditya.bhagwat
Browse files

Update use cases

parent f5ccdf08
Pipeline #130854 passed with stages
in 44 seconds
......@@ -23,7 +23,6 @@ extended <- extend(targets, -22, +22)
spacers <- extended %>% find_spacers(bsgenome)
spacers %<>% add_specificity(extended, bsgenome)
spacers %<>% add_efficiency(bsgenome, method = 'Doench2016')
spacers %>% subset(seqnames == 'chr1') %>%
......@@ -40,6 +39,7 @@ spacers2
targets %<>% subset(targetname %in% c('T0050')) # T0151
extended%<>% subset(targetname %in% c('T0050'))
spacers %<>% subset(targetname %in% c('T0050'))
spacers %>% extract(c(length(.), 1))
# Create plots: original
p <- plot_intervals(targets, color_var = 'targetname') +
......@@ -91,7 +91,7 @@ plot_intervals(gr, facet_var = c('seqnames', 'targetname'))
spacers <- gr %>% find_pe_spacers(bsgenome, nrt=48) %>% add_genome_counts()
spacers$specific <- spacers$G0==1
spacers %>% add_efficiency(bsgenome, 'Doench2016')
spacers %<>% add_efficiency(bsgenome, 'Doench2016')
# Select HBB
gr %<>% extract('HBB')
......
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