Keep abundant transcripts

keep_abundant() 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 columns for the statistics from the hypothesis test.

keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

# S4 method for class 'spec_tbl_df'
keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

# S4 method for class 'tbl_df'
keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

# S4 method for class 'tidybulk'
keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

# S4 method for class 'SummarizedExperiment'
keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

# S4 method for class 'RangedSummarizedExperiment'
keep_abundant(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  factor_of_interest = NULL,
  minimum_counts = 10,
  minimum_proportion = 0.7
)

Arguments

.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))

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

factor_of_interest

The name of the column of the factor of interest. This is used for defining sample groups for the filtering process. It uses the filterByExpr function from edgeR.

minimum_counts

A real positive number. It is the threshold of count per million that is used to filter transcripts/genes out from the scaling procedure.

minimum_proportion

A real positive number between 0 and 1. It is the threshold of proportion of samples for each transcripts/genes that have to be characterised by a cmp bigger than the threshold to be included for scaling procedure.

Value

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A consistent object (to the input) with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A consistent object (to the input) 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

Details

questioning

At the moment this function uses edgeR (DOI: 10.1093/bioinformatics/btp616)

Underlying method: edgeR::filterByExpr( data, min.count = minimum_counts, group = string_factor_of_interest, min.prop = minimum_proportion )

Examples

  keep_abundant(
  tidybulk::se_mini
  )
#> No group or design set. Assuming all samples belong to one group.
#> class: SummarizedExperiment 
#> dim: 182 5 
#> metadata(0):
#> assays(1): count
#> rownames(182): ACAP1 ACP5 ... ZNF286A ZNF324
#> rowData names(2): entrez .abundant
#> colnames(5): SRR1740034 SRR1740035 SRR1740043 SRR1740058 SRR1740067
#> colData names(5): Cell.type time condition days dead