| adjust_abundance,spec_tbl_df-method {tidybulk} | R Documentation |
adjust_abundance
## S4 method for signature 'spec_tbl_df' adjust_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL, log_transform = TRUE, action = "add", ... )
.data |
A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | |
.formula |
A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_intrest + batch) |
.sample |
The name of the sample column |
.transcript |
The name of the transcript/gene column |
.abundance |
The name of the transcript/gene abundance column |
log_transform |
A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data) |
action |
A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get). |
... |
Further parameters passed to the function sva::ComBat |
A 'tbl' with additional columns for the adjusted counts as '<COUNT COLUMN>_adjusted'