newCapSet: Create a new CapSet object

In icetea: Integrating Cap Enrichment with Transcript Expression Analysis

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)

icetea documentation built on Nov. 8, 2020, 6:57 p.m.