read_counts_expt: Read a bunch of count tables and create a usable data frame...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Read a bunch of count tables and create a usable data frame from them.

Description

It is worth noting that this function has some logic intended for the elsayed lab's data storage structure. It shouldn't interfere with other usages, but it attempts to take into account different ways the data might be stored.

Usage

read_counts_expt(
  ids,
  files,
  header = FALSE,
  include_summary_rows = FALSE,
  all.x = TRUE,
  all.y = FALSE,
  merge_type = "merge",
  suffix = NULL,
  countdir = NULL,
  tx_gene_map = NULL,
  file_type = NULL,
  ignore_tx_version = TRUE,
  ...
)

Arguments

ids	List of experimental ids.
files	List of files to read.
header	Whether or not the count tables include a header row.
include_summary_rows	Whether HTSeq summary rows should be included.
all.x	When merging (as opposed to join), choose the x data column.
all.y	When merging (as opposed to join), choose the y data column.
merge_type	Choose one, merge or join.
suffix	Optional suffix to add to the filenames when reading them.
countdir	Optional count directory to read from.
tx_gene_map	Dataframe which provides a mapping between transcript IDs and gene IDs.
file_type	Short circuit the file format autodetection.
ignore_tx_version	Pass along TRUE to tximport's parameter ignoreTxIds to alleviate the headaches associated with salmon's stupid transcript ID .x suffix.
...	More options for happy time!

Details

Used primarily in create_expt() This is responsible for reading count tables given a list of filenames. It tries to take into account upper/lowercase filenames and uses data.table to speed things along.

Value

Data frame of count tables.

See Also

[data.table] [create_expt()] [tximport]

Examples

## Not run: 
 count_tables <- hpgl_read_files(as.character(sample_ids), as.character(count_filenames))

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.