EZbakR (version 0.1.0)

ImportIsoformQuant: Import transcript isoform quantification into EZbakRData object

Description

A convenient wrapper to tximport() for importing isoform quantification data into an EZbakRData object. You need to run this before running EstimateIsoformFractions.

Usage

ImportIsoformQuant(
  obj,
  files,
  quant_tool = c("none", "salmon", "sailfish", "alevin", "piscem", "kallisto", "rsem",
    "stringtie"),
  txIn = TRUE,
  ...
)

Value

An EZbakRData object with an additional element in the readcounts

list named "isform_quant_<quant_tool>". It contains TPM, expected_count, and effective length information for each transcript_id and each sample.

Arguments

obj

An EZbakRData object.

files

A named vector of paths to all transcript quantification files that you would like to import. This will be passed as the first argument of tximport::tximport() (also named files). The names of this vector should be the same as the sample names as they appear in the metadf of the EZbakRData object.

quant_tool

String denoting the type of software used to generate the abundances. Will get passed to the type argument of tximport::tximport(). As described in the documentation for tximport 'Options are "salmon", "sailfish", "alevin", "piscem", "kallisto", "rsem", "stringtie", or "none". This argument is used to autofill the arguments below (geneIdCol, etc.) "none" means that the user will specify these columns. Be aware that specifying type other than "none" will ignore the arguments below (geneIdCol, etc.)'. Referenced 'arguments below' can be specified as part of ....

txIn

Whether or now you are providing isoform level quantification files. Alternative (txIn = FALSE) is gene-level quantification. In ImportIsoformQuant, txIn gets passed to BOTH the txIn and txOut parameters in tximport().

...

Additional arguments to be passed to tximport::tximport(). Especially relevant if you set quant_tool to "none".

Examples

# Dependencies for example
library(dplyr)
library(data.table)

# Simulate and analyze data
simdata <- EZSimulate(30)
ezbdo <- EZbakRData(simdata$cB, simdata$metadf)
ezbdo <- EstimateFractions(ezbdo)

# Hack to generate example quantification files
savedir <- tempdir()
rsem_data <- tibble(
  transcript_id = paste0("tscript_feature", 1:30),
  gene_id = paste0("feature", 1:30),
  length = 1000,
  effective_length = 1000,
  expected_count = 1000,
  TPM = 10,
  FPKM = 10,
  IsoPct = 1
)

fwrite(rsem_data, file.path(savedir, "Sample_1.isoforms.results"), sep = '\t')

files <- file.path(savedir,"Sample_1.isoforms.results")
names(files) <- "Sample_1"

# Read in file
ezbdo <- ImportIsoformQuant(ezbdo, files, quant_tool = "rsem")