Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
# exit if user doesn't have synapser, a log in, or access to data.
if (genieBPC:::.is_connected_to_genie() == FALSE){
knitr::knit_exit()
}
## ---- include=FALSE, eval=genieBPC:::.is_connected_to_genie()-----------------
library(genieBPC)
library(dplyr)
library(tibble)
library(magrittr)
library(gt)
set_synapse_credentials()
## ----echo = FALSE, warning = FALSE, message = FALSE, eval=genieBPC:::.is_connected_to_genie()----
tibble::tribble(
~Argument, ~Description,
"`cohort`", "Vector or list specifying the cohort(s) of interest. Must be one of 'NSCLC' (Non-Small Cell Lung Cancer), 'CRC' (Colorectal Cancer), or 'BrCa' (Breast Cancer)",
"`version`", "Vector specifying the version of the data. Must be one of the following: 'v1.1-consortium', 'v1.2-consortium', 'v2.1-consortium', 'v2.0-public'. When entering multiple cohorts, the order of the version numbers corresponds to the order that the cohorts are specified; the cohort and version number must be in the same order in order to pull the correct data.",
"`download_location`", "If `NULL` (default), data will be returned as a list of dataframes with requested data as list items. Otherwise, specify a folder path to have data automatically downloaded there. When a path is specified, data are not read into the R environment.",
"`username`", "Synapse username",
"`password`", "Synapse password"
) %>%
gt::gt() %>%
gt::fmt_markdown(columns = c(Argument)) %>%
gt::tab_options(table.font.size = 'small',
data_row.padding = gt::px(1),
summary_row.padding = gt::px(1),
grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1),
source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
## ---- eval = FALSE------------------------------------------------------------
# nsclc_2_0 = pull_data_synapse("NSCLC", version = "v2.0-public")
## ---- include = FALSE, eval=genieBPC:::.is_connected_to_genie()---------------
nsclc_2_0 = pull_data_synapse("NSCLC", version = "v2.0-public")
## ---- include = FALSE, eval=genieBPC:::.is_connected_to_genie()---------------
ls(nsclc_2_0$NSCLC_v2.0) %>%
as.data.frame() %>%
mutate(clinical_vs_genomic = case_when(. %in% c("cna", "fusions",
"mutations_extended") ~ "Genomic Data",
TRUE ~ "Clinical Data")) %>%
gt::gt() %>%
gt::cols_label(.data = .,
`.` = md("**Datasets Returned**"),
clinical_vs_genomic = md("**Clinical/Genomic Data**"))
## ---- eval = FALSE------------------------------------------------------------
# pull_data_synapse(c("NSCLC", "CRC"),
# version = c("v2.1-consortium","v1.1-consortium"))
## ---- eval = FALSE------------------------------------------------------------
# pull_data_synapse(c("NSCLC", "CRC"),
# version = c("v1.2-consortium", "v1.1-consortium"))
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