norm_cpm: CPM normalization
In dongzhuoer/rexseek: Matrix Processing in the exSeek Project

Description Usage Arguments Details Value exception See Also Examples

CPM normalization using counts sum of certain genes as scaling factor.

norm_cpm_total(mat)

norm_cpm_top(mat, top_n)

norm_cpm_rm(mat, gene_type)

norm_cpm_refer(mat, refer_gene_id)

`mat`	integer matrix. counts.
`top_n`	integer scalar. See `norm_cpm_top()` below.
`gene_type`	character. See `norm_cpm_rm()` below.
`refer_gene_id`	character. Ensembl transcript id, see `norm_cpm_refer()` below.

norm_cpm_total() uses total genes

norm_cpm_top() uses top 20 genes sorted by counts (assuming top_n = 20L).

norm_cpm_rm() uses non-piRNA genes (assuming gene_type = 'piRNA').

norm_cpm_refer() uses given reference genes

numerical matrix. normalized counts.

some functions may throw errors.

Other matrix normalization: norm_SCnorm, norm_scater

norm_cpm_total(sim_mat) %>% head()

norm_cpm_top(sim_mat, 20L) %>% head()

norm_cpm_rm(sim_mat, c('miRNA', 'piRNA')) %>% head()

norm_cpm_refer(sim_mat, suggest_refer$id) %>% head()