newCapSet {icetea} | R Documentation

## Create a new CapSet object

### Description

The function creates an object of class 'CapSet', used for the TSS analysis. A CapSet object can be created using the the raw, multiplxed fastq files along with the list of sample indexes and corresponding sample names. In case the files are already de-multiplexed or mapped, the CapSet object can also be created using the path to demultiplexed fastq/mapped or filtered BAM files, along with corresponding sample names. In these cases statistics and operations for the missing files would not be possible.

### Usage

    newCapSet(
      expMethod,
      fastq_R1 = NULL,
      fastq_R2 = NULL,
      idxList = NULL,
      sampleNames,
      demult_R1 = NA,
      demult_R2 = NA,
      mapped_file = NA,
      filtered_file = NA,
      paired_end = TRUE
    )

### Arguments

`expMethod` | experiment method ('CAGE', 'RAMPAGE' or 'MAPCap')
`fastq_R1` | path for Read R1 (or file path for single end reads)
`fastq_R2` | path for Read R2 (for paired end reads)
`idxList` | a vector of index sequences (for demultiplexing)
`sampleNames` | (required) a vector of sample names corresponding to the provided files
`demult_R1` | a vector of file paths for demultiplexed R1 reads
`demult_R2` | a vector of file paths for demultiplexed R2 reads
`mapped_file` | a vector of file paths for mapped BAM files.
`filtered_file` | a vector of file paths for de-duplicated BAM files.
`paired_end` | logical, indiciting whether the data is paired end

### Value

An object of class CapSet

### Slots

`fastqType`

  Type of fastq ('single' or 'paired')

`fastq_R1`

  Path to R1 fastq

`fastq_R2`

  Path to R1 fastq (for paired-end data)

`expMethod`

  Name of protocol (RAMPGE or MAPCap)

`sampleInfo`

  A DataFrame object created using information from `newCapSet` function

`tss_detected`

  A GRangesList object of detected TSS

### Examples

    # list of barcode IDs
    idxlist <- c("CAAGTG", "TTAGCC", "GTGGAA", "TGTGAG")

    dir <- system.file("extdata", package="icetea")
    # corresponding sample names
    fnames <- c("embryo1", "embryo2", "embryo3", "embryo4")

    ## CapSet object from raw (multiplexed) fastq files
    cs <- newCapSet(expMethod = 'MAPCap',
           fastq_R1 = file.path(dir, 'mapcap_test_R1.fastq.gz'),
           fastq_R2 = file.path(dir, 'mapcap_test_R2.fastq.gz'),
           idxList = idxlist,
           sampleNames = fnames)

    ## CapSet object from mapped BAM files
    bams <- list.files(file.path(dir, 'bam'), pattern = '.bam$', full.names = TRUE)
    cs <- newCapSet(expMethod = 'MAPCap',
           mapped_file = bams,
           sampleNames = fnames)

[Package icetea version 1.8.0 Index]