impute_missing_abundance {tidybulk} | R Documentation |
impute_missing_abundance() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with an edditional adjusted abundance column. This method uses scaled counts if present.
impute_missing_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL ) ## S4 method for signature 'spec_tbl_df' impute_missing_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL ) ## S4 method for signature 'tbl_df' impute_missing_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL ) ## S4 method for signature 'tidybulk' impute_missing_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL ) ## S4 method for signature 'SummarizedExperiment' impute_missing_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL ) ## S4 method for signature 'RangedSummarizedExperiment' impute_missing_abundance( .data, .formula, .sample = NULL, .transcript = NULL, .abundance = NULL )
.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 |
This function imputes the abundance of missing sample-transcript pair using the median of the sample group defined by the formula
A 'tbl' non-sparse abundance
A 'tbl' with imputed abundance
A 'tbl' with imputed abundance
A 'tbl' with imputed abundance
A 'SummarizedExperiment' object
A 'SummarizedExperiment' object
res = impute_missing_abundance( tidybulk::counts_mini, ~ condition, .sample = sample, .transcript = transcript, .abundance = count )