mp_rrarefy {MicrobiotaProcess} | R Documentation |
mp_rrarefy method
mp_rrarefy( .data, .abundance = NULL, raresize, trimOTU = FALSE, trimSample = FALSE, seed = 123, ... ) ## S4 method for signature 'MPSE' mp_rrarefy( .data, .abundance = NULL, raresize, trimOTU = FALSE, trimSample = FALSE, seed = 123, ... ) ## S4 method for signature 'tbl_mpse' mp_rrarefy( .data, .abundance = NULL, raresize, trimOTU = FALSE, trimSample = FALSE, seed = 123, ... ) ## S4 method for signature 'grouped_df_mpse' mp_rrarefy( .data, .abundance = NULL, raresize, trimOTU = FALSE, trimSample = FALSE, seed = 123, ... )
.data |
MPSE or tbl_mpse object |
.abundance |
the name of OTU(feature) abundance column, default is Abundance. |
raresize |
integer Subsample size for rarefying community. |
trimOTU |
logical Whether to remove the otus that are no longer present in any sample after rarefaction |
trimSample |
logical whether to remove the samples that do not have enough abundance (raresize), default is FALSE. |
seed |
a random seed to make the rrarefy reproducible, default is 123. |
... |
additional parameters, meaningless now. |
update object
Shuangbin Xu
[mp_extract_assays()] and [mp_decostand()]
data(mouse.time.mpse) mouse.time.mpse %>% mp_rrarefy()