hpgl_norm: Normalize a dataframe/expt, express it, and/or transform it

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

Normalize a dataframe/expt, express it, and/or transform it

Description

There are many possible options to this function. Refer to normalize_expt() for a more complete list.

Usage

hpgl_norm(data, ...)

Arguments

data	Some data as a df/expt/whatever.
...	I should put all those other options here

Value

edgeR's DGEList expression of a count table. This seems to me to be the easiest to deal with.

See Also

[edgeR] [DESeq2] [edgeR::cpm()] [filter_counts()] [batch_counts()] [convert_counts()] [transform_counts()]

Examples

## Not run: 
 df_raw = hpgl_norm(expt = expt)  ## Only performs low-count filtering
 df_raw = hpgl_norm(df = a_df, design = a_design) ## Same, but using a df
 df_ql2rpkm = hpgl_norm(expt = expt, norm='quant', transform='log2',
                        convert='rpkm')  ## Quantile, log2, rpkm
 count_table = df_ql2rpkm$counts

## End(Not run)

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