Description Usage Arguments Value Note
loads expression data in GxS format, with one row per gene & one column per sample returns a tbl_df also in GxS format, with sample-batch-assignment in attr 'sampleinfo'
1 2 | load_expdata(path, gene_col = "Gene_symbol", data_loader = readr::read_tsv,
batch = 1, filter = NULL, trans = NULL, ...)
|
path |
(chr) path to expression matrix |
gene_col |
(chr) name of column containing gene symbol |
data_loader |
(function) function to use when loading data |
batch |
(chr) optional description to give this batch |
... |
extra args to data_loader |
expression_filter |
(dbl) optional value by which to filter expression (if NULL, no filter) |
tbl_df containing expression data, with columns '_SAMPLE_ID' and '_BATCH'
Expects data in format prepared by prep_gene_expression_matrix.R
Genes are filtered to remove those with 0 expression across all samples these can be filled in with 0 if expressed in at least one batch on combination
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