deseq_wide: Obtain DESeq object from raw counts wide dataframe.

In mirvie/mirmisc: Non-Modeling Helper Functions For Mirvie R Coders

Description

Wide is samples in columns, genes in rows.

Usage

deseq_wide(data, design, compvar)

Arguments

data	A wide datafame with raw counts that contains raw counts for samples of interest (may contain other samples as well, which will be filtered out).
design	A dataframe with all of the variables specified in compvar as column names. Must have the same number of rows as data with samples in the same order.
compvar	a character vector with the name(s) of the variable(s), which must be identical to the variable name(s) in the design dataframe.

Value

A DESeq2 object.

See Also

Other Arkady: check_sample_descs(), collapse_tech_reps(), deseq_contrasts(), deseq_pairs(), fgsea_basic(), plot_cond_paired_pearson(), plot_down(), plot_metrics_global(), plot_var_mean_ratio(), prep_gsea_input_gene_set(), prep_gsea_input_lfc(), prep_rd_input(), reconcile_names()

Examples

rs_genes <- arrow::read_feather(
  system.file("extdata", "rs_genes_draw_3_4.feather", package = "mirmisc")
)
rs_meta <- arrow::read_feather(
  system.file("extdata", "rs_meta_draw_3_4.feather", package = "mirmisc")
)
deseq_wide(rs_genes, rs_meta, compvar = "meta_draw")

mirvie/mirmisc documentation built on Dec. 21, 2021, 7 p.m.