In PeterDeWeirdt/intactr: Detect Interactions from CRISPR Combinatorial Screens

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 5
)

library(intactr)

Calculate genetic interaction scores for an apoptotic library screened with Cas12a

The data: 22 genes involoved in apoptosis 10 guides per gene 20 olfactory receptor controls columns gene1, guide1, guide2, control1, control2

knitr::kable(head(apop_combo_lfcs))

We calculate score for combinations by taking the residual from a line fit to each guide. For example, here are the residual plots for all guides tragetting BCL2L1 and MCL1

plot_data <- plot_combo_residuals('BCL2L1', 'MCL1', apop_combo_lfcs, 10)
plot_data$plot

combo_scores <- calculate_anchor_residuals(apop_combo_lfcs, 10)
knitr::kable(head(combo_scores))

plot_score_heatmap(combo_scores, 'combo_z_score')

Our strongest hits include well known interactors as well as novel hits.

plot_hit_network(combo_scores, 'combo_z_score', 5)

One particularly interesting novel hit is the one between WSB2 and MARCH5

plot_combo('WSB2', 'MARCH5', apop_combo_lfcs)

PeterDeWeirdt/intactr documentation built on June 8, 2020, 1:52 p.m.