Read GlyHunter result

This function reads in a GlyHunter result file and returns a glyexp::experiment() object.

Usage

read_glyhunter(
  fp,
  sample_info = NULL,
  glycan_type = c("N", "O"),
  sample_name_converter = NULL
)

Arguments

fp: File path of the GlyHunter result file.
sample_info: File path of the sample information file (csv), or a sample information data.frame/tibble.
glycan_type: Glycan type. Either "N" or "O". Default is "N".
sample_name_converter: A function to convert sample names from file paths. The function should take a character vector of old sample names and return new sample names. Note that sample names in sample_info should match the new names. If NULL, original names are kept.

Value

An glyexp::experiment() object.

Which file to use?

Use the "summary_area.csv" file in the GlyHunter result folder. No edit is necessary.

Output

This function returns a glyexp::experiment() object. The variable information tibble has one column: "glycan_composition" as a glyrepr::glycan_composition() object.

Sample information

The sample information file should be a csv file with the first column named sample, and the rest of the columns being sample information. The sample column must match the RawName column in the pGlyco3 result file, although the order can be different.

You can put any useful information in the sample information file. Recommended columns are:

group: grouping or conditions, e.g. "control" or "tumor", required for most downstream analyses
batch: batch information, required for batch effect correction