Description Usage Arguments Details Value exception See Also Examples
CPM normalization using counts sum of certain genes as scaling factor.
1 2 3 4 5 6 7 | 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 |
gene_type |
character. See |
refer_gene_id |
character. Ensembl transcript id, see |
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
1 2 3 4 5 6 7 | 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()
|
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