fill_missing_abundance | 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 |
questioning
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
print("Not run for build time.")
# tidybulk::se_mini |> fill_missing_abundance( fill_with = 0)
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