extract_abundance: Add differential transcription information to a tbl using...

In stemangiola/ttSc: Friendly tidy wrappers for facilitating transcriptional analyses

Add differential transcription information to a tbl using edgeR.

Description

extract_abundance() takes as imput a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with additional columns for the statistics from the hypothesis test.

Usage

extract_abundance(
  .data,
  transcripts = NULL,
  all = F,
  exclude_zeros = F,
  shape = "long",
  action = "add"
)

Arguments

.data	A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
action	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).
.formula	A formula with no response variable, representing the desired linear model
.sample	The name of the sample column
.transcript	The name of the transcript/gene column
.abundance	The name of the transcript/gene abundance column
significance_threshold	A real between 0 and 1 (usually 0.05).

Details

\lifecycle

experimental

At the moment this function uses edgeR only, but other inference algorithms will be added in the near future.

Value

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

Examples

	extract_abundance(
	    ~ condition,
	    sample,
	    transcript,
	    `count`
	)

stemangiola/ttSc documentation built on Dec. 8, 2022, 2:37 a.m.