rawAlignment {KnowSeq} | R Documentation

## rawAlignment allows downloading and processing the fastq samples in a CSV file.

### Description

This function allows downloading and processing the fastq samples in a CSV file. Also, different alignment methods can be used such as Hisat2, Salmon and Kallisto. Finally, the function can downloads the reference files required: FASTA Reference Genome and GTF file.

### Usage

    rawAlignment(
      data,
      seq = "hisat2",
      downloadRef = FALSE,
      downloadSamples = FALSE,
      createIndex = TRUE,
      BAMfiles = TRUE,
      SAMfiles = TRUE,
      countFiles = TRUE,
      referenceGenome = 38,
      customFA = "",
      customGTF = "",
      fromGDC = FALSE,
      tokenPath = "",
      manifestPath = "",
      tx2Counts = ""
    )

### Arguments

`data` | The ID of the variable which contains the samples. Our recommendation is to load this variable from a CSV file.
`seq` | This parameter represents the alignment method that will be used in the process. The possibilities are "hisat2" "salmon" and "kallisto".
`downloadRef` | A logical parameter that represents if the reference files will be downloaded or not.
`downloadSamples` | A logical parameter that represents if the samples of the CSV file will be downloaded or not.
`createIndex` | A logical parameter that represents if the index of the aligner would be created or not.
`BAMfiles` | A logical parameter that represents if the you want the BAM files or not.
`SAMfiles` | A logical parameter that represents if the you want the SAM files or not.
`countFiles` | A logical parameter that represents if the you want the Count files or not.
`referenceGenome` | This parameter allows choosing the reference genome that will be used for the alignment. The options are 37,38 or custom. The two first are human genomes, but with the third option you can choose any genome stored in the computer.
`customFA` | The path to the custom FASTA file of the reference genome.
`customGTF` | The path to the custom GTF file.
`fromGDC` | A logical parameter that allows processing BAM files from GDC portal by using the custom reference genome from GDC.
`tokenPath` | The path to the GDC portal user token. It is required to downloads the controlled BAM files.
`manifestPath` | The path to the manifest with the information required to downloads the controlled BAM files selected in GDC Portal.
`tx2Counts` | A matrix with two columns that contains the conversion of transcripts ID to genes ID. There is more information in the function `tximport`. This parameter is only required with salmon and kallisto.

### Value

Nothing to return.

### Examples

    # Due to the high computational cost, we strongly recommend it to see the offical documentation and the complete example included in this package:

    dir <- system.file("extdata", package="KnowSeq")

    #Using read.csv for NCBI/GEO files (read.csv2 for ArrayExpress files)
    GSE74251csv <- read.csv(paste(dir,"/GSE74251.csv",sep = ""))

    ## Not run: rawAlignment(GSE74251csv,seq="hisat2",downloadRef=FALSE,downloadSamples=FALSE, createIndex = TRUE, BAMfiles = TRUE, SAMfiles = TRUE, countFiles = TRUE, referenceGenome = 38, customFA = "", customGTF = "", fromGDC = FALSE, tokenPath = "", manifestPath = "",tx2Counts = "")

[Package KnowSeq version 1.1.27 Index]