Nothing
## ----setup, include=FALSE, echo=FALSE-----------------------------------------
# knitr::knit_hooks$set(optipng = knitr::hook_optipng)
# knitr::opts_chunk$set(optipng = '-o7')
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(fig.align = "center")
knitr::opts_chunk$set(fig.width = 12)
knitr::opts_chunk$set(fig.height = 6)
library(immunarch)
# source("../R/testing.R")
# immdata = load_test_data()
data(immdata)
## ---- eval=F------------------------------------------------------------------
# #path argument is a path to the folder with your file or files including the metadata file.
# immdata <- repLoad(path)
## ---- eval=F------------------------------------------------------------------
# immdata <- repLoad('example')
## ---- eval=F------------------------------------------------------------------
# #path to the folder with example data
# file_path = paste0(system.file(package="immunarch"), "/extdata/io/")
# immdata <- repLoad(file_path)
## ---- eval=F------------------------------------------------------------------
# # For instance you have a following structure in your folder:
# # >_ ls
# # immunoseq1.txt
# # immunoseq2.txt
# # immunoseq3.txt
# # metadata.txt
## ---- eval=F------------------------------------------------------------------
# # To load the whole folder with every file in it type:
# file_path = paste0(system.file(package="immunarch"), "/extdata/io/")
# immdata <- repLoad(file_path)
# print(names(immdata))
#
# # In order to do that your folder must contain metadata file named
# # "metadata.txt".
#
# # In R, when you load your data:
# # > immdata <- repLoad("path/to/your/folder/")
# # > names(immdata)
# # [1] "data" "meta"
#
# # Suppose you do not have "metadata.txt":
# # > immdata <- repLoad("path/to/your/folder/")
# # > names(immdata)
# # [1] "data" "meta"
#
## -----------------------------------------------------------------------------
as_tibble(data.frame(Sample = c("immunoseq1", "immunoseq2", "immunoseq3"), stringsAsFactors = F))
## ---- eval=F------------------------------------------------------------------
# # Your list of repertoires in immunarch's format
# DATA
# # Metadata data frame
# META
#
# # Create a temporary directory
# dbdir = tempdir()
#
# # Create a DBI connection to MonetDB in the temporary directory.
# con = DBI::dbConnect(MonetDBLite::MonetDBLite(), embedded = dbdir)
#
# # Write each repertoire to MonetDB. Each table has corresponding name from the DATA
# for (i in 1:length(DATA)) {
# DBI::dbWriteTable(con, names(DATA)[i], DATA[[i]], overwrite=TRUE)
# }
#
# # Create a source in the temporary directory with MonetDB
# ms = MonetDBLite::src_monetdblite(dbdir = dbdir)
# res_db = list()
#
# # Load the data from MonetDB to dplyr tables
# for (i in 1:length(DATA)) {
# res_db[[names(DATA)[i]]] = dplyr::tbl(ms, names(DATA)[i])
# }
#
# # Your data is ready to use
# list(data = res_db, meta = META)
## ----basic-data---------------------------------------------------------------
top(immdata$data[[1]])
## ---- eval=FALSE--------------------------------------------------------------
# coding(immdata$data[[1]])
## ---- eval=FALSE--------------------------------------------------------------
# noncoding(immdata$data[[1]])
## ---- eval=FALSE--------------------------------------------------------------
# nrow(inframes(immdata$data[[1]]))
## ---- eval=FALSE--------------------------------------------------------------
# nrow(outofframes(immdata$data[[1]]))
## -----------------------------------------------------------------------------
filter(immdata$data[[1]], V.name == 'TRBV10-1')
## -----------------------------------------------------------------------------
ds = repSample(immdata$data, "downsample", 100)
sapply(ds, nrow)
## -----------------------------------------------------------------------------
ds = repSample(immdata$data, "sample", .n = 10)
sapply(ds, nrow)
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.