fill_missing_abundance {tidybulk} | R Documentation |
fill_missing_abundance() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' 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 ) ## S4 method for signature 'SummarizedExperiment' fill_missing_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, fill_with ) ## S4 method for signature 'RangedSummarizedExperiment' 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 'tbl' non-sparse abundance
A 'tbl' with filled abundance
A 'tbl' with filled abundance
A 'tbl' with filled abundance
A 'SummarizedExperiment' object
A 'SummarizedExperiment' object
fill_missing_abundance(tidybulk::counts_mini, sample, transcript, count, fill_with = 0)