fill_missing_abundance {tidybulk} | R Documentation |
fill_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 new observations
fill_missing_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, fill_with ) ## S4 method for signature 'spec_tbl_df' fill_missing_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, fill_with ) ## S4 method for signature 'tbl_df' fill_missing_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, fill_with ) ## S4 method for signature 'tidybulk' fill_missing_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, fill_with )
.data |
A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | |
.sample |
The name of the sample column |
.transcript |
The name of the transcript column |
.abundance |
The name of the transcript abundance column |
fill_with |
A numerical abundance with which fill the missing data points |
This function fills 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 filled abundance
A consistent object (to the input) with filled abundance
A consistent object (to the input) with filled abundance
tidybulk::se_mini |> tidybulk() |> fill_missing_abundance( fill_with = 0)