write_expr_annot: Get expression and annotation tables

Description Usage Arguments

Description

This function takes a vector of GEO study IDs, selects those with only one platform and those with samples within a given range. It then uses the collapse_rows function to collapse probes, and finally writes the expression and annotation data to files in the given directory.

Usage

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write_expr_annot(gse_ids, min_samples = 15, max_samples = 200,
  directory = file.path(getwd(), "data"), force = FALSE,
  force_repeat = FALSE, get_expr = TRUE, get_annot = TRUE)

Arguments

gse_ids

A character vector containing GEO study accession IDs

min_samples

The minimum number of samples for studies (inclusive)

max_samples

The maximum number of samples for studies (inclusive)

directory

The directory to save files

force

If TRUE, overwrites the given directory.

force_repeat

If FALSE, avoids downloading study data already present in the 'directory' folder (as informed by folder names).

get_expr

If TRUE, get expression data.

get_annot

If TRUE, get annotation data.


pedrostrusso/cemitooldb documentation built on May 25, 2019, 11:34 p.m.