Nothing
## ----install, eval=FALSE------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install("infercnv")
## ----install-optionals, eval = FALSE------------------------------------------
# install.packages("tibble")
#
# install.packages("devtools")
# devtools::install_github("bmbroom/tsvio")
# devtools::install_github("bmbroom/NGCHMR", ref="stable")
# devtools::install_github("broadinstitute/inferCNV_NGCHM")
#
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
library(infercnv)
## -----------------------------------------------------------------------------
infercnv_obj = CreateInfercnvObject(
raw_counts_matrix="../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz",
annotations_file="../inst/extdata/oligodendroglioma_annotations_downsampled.txt",
delim="\t",
gene_order_file="../inst/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt",
ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)"))
## ---- results="hide"----------------------------------------------------------
out_dir = tempfile()
infercnv_obj_default = infercnv::run(
infercnv_obj,
cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
out_dir=out_dir,
cluster_by_groups=TRUE,
plot_steps=FALSE,
denoise=TRUE,
HMM=FALSE,
no_prelim_plot=TRUE,
png_res=60
)
## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics(paste(out_dir, "infercnv.png", sep="/"))
## ----sessioninfo, echo=FALSE, tidy=TRUE, tidy.opts=list(width.cutoff=60), out.width=60----
sessionInfo()
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