keep_variable {tidybulk} | R Documentation |
keep_variable() takes as imput a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with additional columns for the statistics from the hypothesis test.
keep_variable( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, top = 500, log_transform = TRUE ) ## S4 method for signature 'spec_tbl_df' keep_variable( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, top = 500, log_transform = TRUE ) ## S4 method for signature 'tbl_df' keep_variable( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, top = 500, log_transform = TRUE ) ## S4 method for signature 'tidybulk' keep_variable( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, top = 500, log_transform = TRUE ) ## S4 method for signature 'SummarizedExperiment' keep_variable( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, top = 500, log_transform = TRUE ) ## S4 method for signature 'RangedSummarizedExperiment' keep_variable( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, top = 500, log_transform = TRUE )
.data |
A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | |
.sample |
The name of the sample column |
.transcript |
The name of the transcript/gene column |
.abundance |
The name of the transcript/gene abundance column |
top |
Integer. Number of top transcript to consider |
log_transform |
A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data) |
At the moment this function uses edgeR only, but other inference algorithms will be added in the near future.
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).
A 'SummarizedExperiment' object
A 'SummarizedExperiment' object
keep_variable( tidybulk::counts_mini, sample, transcript, `count`, top = 500 )