impute_missing_abundance {tidybulk} | R Documentation |
impute_missing_abundance() takes as input A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and returns a consistent object (to the input) with additional sample-transcript pairs with imputed transcript abundance.
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) ## S4 method for signature 'RangedSummarizedExperiment' impute_missing_abundance(.data, .formula)
.data |
A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) |
.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_interest + 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 |
'r lifecycle::badge("maturing")'
This function imputes the abundance of missing sample-transcript pair using the median of the sample group defined by the formula
A consistent object (to the input) non-sparse abundance
A consistent object (to the input) with imputed abundance
A consistent object (to the input) with imputed abundance
A consistent object (to the input) with imputed abundance
A 'SummarizedExperiment' object
A 'SummarizedExperiment' object
res = impute_missing_abundance( tidybulk::se_mini, ~ condition )