inspectFromBAM: Wrapper function from BAM files

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

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

inspectFromBAM(
  txdb,
  annotation_table,
  labeling_time = NULL,
  strandSpecific = 0,
  isPairedEnd = FALSE,
  estimateRatesWith = "der",
  useSigmoidFun = TRUE,
  file = NULL
)

Arguments

txdb	A TranscriptDB object for the selected organism
annotation_table	Paths and experimental design associated to bam files. 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). In case 'annotation_table' has 2 colums named 'condition' and 'total', INSPEcT- analysis is run. In case 'annotation_table' has 3 colums named 'condition', 'total' and 'nascent', INSPEcT+ analysis is run. 'condition' is a colums 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' and 'nascent' contains the path to totalRNA and nascentRNA BAM files, respectively.
labeling_time	A numeric indicating the time of labeling exposure to the modified nucleotide. To be indicated only in case of INSPEcT+ analysis.
strandSpecific	A numeric indicating the strandness of the BAM files, 0 for non strand-specific, 1 for stranded, 2 for reversely-stranded. 0 by default.
isPairedEnd	A logical indicating if paired-end sequencing have been performed. FALSE by default.
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.

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.