UCSCXenaTools (version 1.6.1)

XenaPrepare: Prepare (Load) Downloaded Datasets to R

Description

Prepare (Load) Downloaded Datasets to R

Usage

XenaPrepare(
  objects,
  objectsName = NULL,
  use_chunk = FALSE,
  chunk_size = 100,
  subset_rows = TRUE,
  select_cols = TRUE,
  callback = NULL,
  comment = "#",
  na = c("", "NA", "[Discrepancy]"),
  ...
)

Value

a list contains file data, which in way of tibbles

Arguments

objects

a object of character vector or data.frame. If objects is data.frame, it should be returned object of XenaDownload function. More easier way is that objects can be character vector specify local files/directory and download urls.

objectsName

specify names for elements of return object, i.e. names of list

use_chunk

default is FALSE. If you want to select subset of original data, please set it to TRUE and specify corresponding arguments: chunk_size, select_direction, select_names, callback.

chunk_size

the number of rows to include in each chunk

subset_rows

logical expression indicating elements or rows to keep: missing values are taken as false. x can be a representation of data frame you wanna do subset operation. Of note, the first colname of most of datasets in Xena will be set to "sample", you can use it to select rows.

select_cols

expression, indicating columns to select from a data frame. 'x' can be a representation of data frame you wanna do subset operation, e.g. select_cols = colnames(x)[1:3] will keep only first to third column.

callback

a function to call on each chunk, default is NULL, this option will overvide operations of subset_rows and select_cols.

comment

a character specify comment rows in files

na

a character vectory specify NA values in files

...

other arguments transfer to read_tsv function or read_tsv_chunked function (when use_chunk is TRUE) of readr package.

Author

Shixiang Wang

Examples

if (FALSE) {
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)

xe_download = XenaDownload(xe_query)
dat = XenaPrepare(xe_download)
}