Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----install, eval=FALSE, echo=TRUE-------------------------------------------
# devtools::install_github(repo = "jeremy37/rgenie")
## ---- message=FALSE-----------------------------------------------------------
library(rgenie)
library(readr, quietly = TRUE) # Not required, but we use it below
library(magrittr, quietly = TRUE)
## ----download_example_x, echo=FALSE, eval=FALSE-------------------------------
# # Note that the get the vignette to pass CRAN's checks, we can't download data
# # as part of the vignette. What we have to do is to provide example data that
# # has the results objects already. But we would like to display to the user
# # how to do everything from the downloaded example. To do this, I echo the
# # code chunks for downloading the example, but don't run them. The results
# # should already be loaded as part of the package data.
## ----download_example, eval=FALSE, echo=TRUE----------------------------------
# rgenie::download_example(dir = "~/genie_example", name = "MUL1")
## ----regions, eval=FALSE, echo=TRUE-------------------------------------------
# mul1_regions = readr::read_tsv("~/genie_example/MUL1/mul1.genie_regions.tsv")
# print(mul1_regions)
## ---- echo=FALSE--------------------------------------------------------------
print(mul1_regions)
## -----------------------------------------------------------------------------
print(mul1_regions$wt_allele_profile)
print(mul1_regions$hdr_allele_profile)
print(mul1_regions$ref_sequence)
## ----replicates, eval=FALSE---------------------------------------------------
# mul1_replicates = readr::read_tsv("~/genie_example/MUL1/mul1.genie_replicates.tsv")
# print(mul1_replicates)
## ---- echo=FALSE--------------------------------------------------------------
print(mul1_replicates)
## ----grep_example, eval=FALSE, echo=TRUE--------------------------------------
# setwd("~/genie_example/MUL1/")
# mul1_grep_results = grep_analysis(mul1_regions,
# mul1_replicates,
# required_match_left = 10,
# required_match_right = 10,
# min_mapq = 0,
# quiet = TRUE)
## -----------------------------------------------------------------------------
length(mul1_grep_results)
grep_result = mul1_grep_results[[1]]
names(grep_result)
## -----------------------------------------------------------------------------
grep_result$region_stats
## -----------------------------------------------------------------------------
grep_result$region_stats$effect
grep_result$region_stats$pval
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::grep_summary_plot(grep_result)
## -----------------------------------------------------------------------------
mul1_replicates = mul1_replicates %>% dplyr::filter(replicate != "c1.1")
## ---- eval=FALSE, echo=TRUE---------------------------------------------------
# setwd("~/genie_example/MUL1/")
# mul1_del_results = rgenie::deletion_analysis(mul1_regions,
# mul1_replicates,
# required_match_left = 10,
# required_match_right = 10,
# crispr_del_window = 100,
# min_mapq = 0,
# max_mismatch_frac = 0.05,
# min_aligned_bases = 50,
# exclude_multiple_deletions = FALSE,
# exclude_nonspanning_reads = TRUE,
# allele_profile = FALSE,
# del_span_start = -20,
# del_span_end = 20,
# quiet = TRUE)
## -----------------------------------------------------------------------------
del_result = mul1_del_results[[1]]
names(del_result)
## -----------------------------------------------------------------------------
tbl = tibble::tibble(Name = names(del_result$region_stats), Value = as.character(del_result$region_stats))
knitr::kable(tbl)
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::deletion_summary_plot(del_result)
del_result$replicate_stats
## -----------------------------------------------------------------------------
del_result$replicate_stats
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::deletion_alleles_plot(del_result,
viewing_window = 40,
color_by="window")
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::deletion_profile_plot(del_result,
viewing_window = 40)
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::replicate_summary_plot(del_result,
outlier_threshold = NA)
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::replicate_qc_plot(del_result,
outlier_threshold = NA)
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::allele_effect_plot(del_result,
viewing_window = 40,
max_alleles = 40)
## ----fig.width=7, fig.height=6------------------------------------------------
all_plots = rgenie::deletion_plots(del_result,
opts = genie_plot_options(),
variance_components_plot = FALSE,
power_plots = FALSE)
names(all_plots)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# pdf("genie_plots.pdf", width=7, height=6)
# print(all_plots)
# dev.off()
## -----------------------------------------------------------------------------
plot_opts = genie_plot_options()
print(plot_opts)
## ----fig.width=7, fig.height=6------------------------------------------------
rgenie::experiment_summary_plot(mul1_grep_results, mul1_del_results)
## ----fig.width=7, fig.height=6------------------------------------------------
grep_tables = rgenie::bind_results(mul1_grep_results)
names(grep_tables)
del_tables = rgenie::bind_results(mul1_del_results)
names(del_tables)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.