R/methods.R
, R/methods_SE.R
adjust_abundance-methods.Rd
adjust_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 an additional adjusted abundance column. This method uses scaled counts if present.
adjust_abundance(
.data,
.formula,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
transform = log1p,
inverse_transform = expm1,
action = "add",
...,
log_transform = NULL
)
# S4 method for spec_tbl_df
adjust_abundance(
.data,
.formula,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
transform = log1p,
inverse_transform = expm1,
action = "add",
...,
log_transform = NULL
)
# S4 method for tbl_df
adjust_abundance(
.data,
.formula,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
transform = log1p,
inverse_transform = expm1,
action = "add",
...,
log_transform = NULL
)
# S4 method for tidybulk
adjust_abundance(
.data,
.formula,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
transform = log1p,
inverse_transform = expm1,
action = "add",
...,
log_transform = NULL
)
# S4 method for SummarizedExperiment
adjust_abundance(
.data,
.formula,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
transform = log1p,
inverse_transform = expm1,
action = "add",
...,
log_transform = NULL
)
# S4 method for RangedSummarizedExperiment
adjust_abundance(
.data,
.formula,
.sample = NULL,
.transcript = NULL,
.abundance = NULL,
transform = log1p,
inverse_transform = expm1,
action = "add",
...,
log_transform = NULL
)
A `tbl` (with at least three columns for sample, feature and transcript abundance) or `SummarizedExperiment` (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_interest + batch)
The name of the sample column
The name of the transcript/gene column
The name of the transcript/gene abundance column
A function that will tranform the counts, by default it is log1p for RNA sequencing data, but for avoinding tranformation you can use identity
A function that is the inverse of transform (e.g. expm1 is inverse of log1p). This is needed to tranform back the counts after analysis.
A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
Further parameters passed to the function sva::ComBat
DEPRECATED - A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)
A consistent object (to the input) with additional columns for the adjusted counts as `<COUNT COLUMN>_adjusted`
A consistent object (to the input) with additional columns for the adjusted counts as `<COUNT COLUMN>_adjusted`
A consistent object (to the input) with additional columns for the adjusted counts as `<COUNT COLUMN>_adjusted`
A consistent object (to the input) with additional columns for the adjusted counts as `<COUNT COLUMN>_adjusted`
A `SummarizedExperiment` object
A `SummarizedExperiment` object
`r lifecycle::badge("maturing")`
This function adjusts the abundance for (known) unwanted variation. At the moment just an unwanted covariate is allowed at a time using Combat (DOI: 10.1093/bioinformatics/bts034)
Underlying method: sva::ComBat(data, batch = my_batch, mod = design, prior.plots = FALSE, ...)
cm = tidybulk::se_mini
cm$batch = 0
cm$batch[colnames(cm) %in% c("SRR1740035", "SRR1740043")] = 1
cm %>%
identify_abundant() |>
adjust_abundance( ~ condition + batch )
#> No group or design set. Assuming all samples belong to one group.
#> Found2batches
#> Adjusting for1covariate(s) or covariate level(s)
#> Standardizing Data across genes
#> Fitting L/S model and finding priors
#> Finding parametric adjustments
#> Adjusting the Data
#> class: SummarizedExperiment
#> dim: 527 5
#> metadata(0):
#> assays(2): count count_adjusted
#> rownames(527): ABCB4 ABCB9 ... ZNF324 ZNF442
#> rowData names(2): entrez .abundant
#> colnames(5): SRR1740034 SRR1740035 SRR1740043 SRR1740058 SRR1740067
#> colData names(6): Cell.type time ... dead batch