scale_abundance {tidybulk} | R Documentation |
scale_abundance() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and Scales transcript abundance compansating for sequencing depth (e.g., with TMM algorithm, Robinson and Oshlack doi.org/10.1186/gb-2010-11-3-r25).
scale_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, method = "TMM", reference_sample = NULL, action = "add", reference_selection_function = NULL ) ## S4 method for signature 'spec_tbl_df' scale_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, method = "TMM", reference_sample = NULL, action = "add", reference_selection_function = NULL ) ## S4 method for signature 'tbl_df' scale_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, method = "TMM", reference_sample = NULL, action = "add", reference_selection_function = NULL ) ## S4 method for signature 'tidybulk' scale_abundance( .data, .sample = NULL, .transcript = NULL, .abundance = NULL, method = "TMM", reference_sample = NULL, action = "add", reference_selection_function = NULL ) ## S4 method for signature 'SummarizedExperiment' scale_abundance(.data, method = "TMM", reference_sample = NULL) ## S4 method for signature 'RangedSummarizedExperiment' scale_abundance(.data, method = "TMM", reference_sample = NULL)
.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 |
method |
A character string. The scaling method passed to the back-end function (i.e., edgeR::calcNormFactors; "TMM","TMMwsp","RLE","upperquartile") |
reference_sample |
A character string. The name of the reference sample. If NULL the sample with highest total read count will be selected as reference. |
action |
A character string between "add" (default) and "only". "add" joins the new information to the input tbl (default), "only" return a non-redundant tbl with the just new information. |
reference_selection_function |
DEPRECATED. please use reference_sample. |
'r lifecycle::badge("maturing")'
Scales transcript abundance compensating for sequencing depth (e.g., with TMM algorithm, Robinson and Oshlack doi.org/10.1186/gb-2010-11-3-r25). Lowly transcribed transcripts/genes (defined with minimum_counts and minimum_proportion parameters) are filtered out from the scaling procedure. The scaling inference is then applied back to all unfiltered data.
Underlying method edgeR::calcNormFactors(.data, method = c("TMM","TMMwsp","RLE","upperquartile"))
A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'
A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'
A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'
A tbl object with additional columns with scaled data as '<NAME OF COUNT COLUMN>_scaled'
A 'SummarizedExperiment' object
A 'SummarizedExperiment' object
tidybulk::se_mini %>% identify_abundant() %>% scale_abundance()