inspectFromPCR {INSPEcT} | R Documentation

## Wrapper function from PCR quantifications

### Description

Function to run the whole INSPEcT differential rate analysis procedure with a single line. The function save the output analysis to file that can be later loaded in the R environment or in the INSPEcT-GUI.

### Usage

    inspectFromPCR(
      totalRNA_table,
      nascentRNA_table = NULL,
      labeling_time = NULL,
      estimateRatesWith = "der",
      useSigmoidFun = TRUE,
      file = NULL
    )

### Arguments

`totalRNA_table` | Exonic quantification, intronic quantification and experimental design associated to totalRNA of a single gene quantified by PCR. They could be provided directly as a 'data.frame', or as a path to the file containing the information. Possible file formats are csv' (comma-separated-values), 'tsv' (comma-separated-values), or 'xls' (Excel). 'totalRNA_table' must have 3 colums named 'condition', 'total_exonic' and 'total_intronic'. 'condition' is a column indicating the experimental condition, a character vector (containing, for example, 'WT' or 'KD') in case of steady-state experiments, or numerical values indicating the time from the unperturbed condition in case of time-course analysis. 'total_exonic' and 'total_intronic' contains abundance of gene measured in its exonic and intronic regions, respectively, in the total RNA fraction.
`nascentRNA_table` | similar to 'totalRNA_table' but referred to nascent RNA fraction. In this case, colums names must be 'condition', 'nascent_exonic' and 'nascent_intronic'. In case this infromation is not provided, INSPEcT- analysis is run. If otherwise this information is present, INSPEcT+ analysis is run.
`labeling_time` | A numeric indicating the time of labeling exposure to the modified nucleotide. To be indicated only in case of INSPEcT+ analysis.
`estimateRatesWith` | Either "int" or "der". With "int" the degradation and processing rates are estimated integrating the system between one time point and the following. With "der" degradation and processing rates are estimated using the derivative of total and pre mRNA. (default is "der")
`useSigmoidFun` | A logical, whether to choose between sigmoid and impulse function to fit rates and concentrations. In case not, always impulse function is used. (default is TRUE)
`file` | A character indicating where the output of the analysis will be stored. If not provided the file name will be created automaticcally and saved on the current folder.

### Examples

    if( Sys.info()["sysname"] != "Windows" ) {
    totalAnnTabPCR <- system.file(package = 'INSPEcT', 'totalAnnTabPCR.csv')
    nascentAnnTabPCR <- system.file(package = 'INSPEcT', 'nascentAnnTabPCR.csv')
    inspectFromPCR(totalAnnTabPCR, nascentAnnTabPCR, labeling_time=1/6)
    }

[Package INSPEcT version 1.22.0 Index]