faseqCount: Construct FASeq Data Set

Description Usage Arguments Details Value References

View source: R/estimate.R

Description

This function quantifies feature signals for location features using CLIP-seq data. You align CLIP-seq reads to the genome and provide FASeq with the resulting bam files. We will take care of the rest.

Usage

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faseqCount(
  event,
  sampleData,
  signal.type = "FPKM",
  FUN.aggregate = "mean",
  minMQS = 10,
  minOverlap = 12,
  isPairedEnd = TRUE,
  cores = max(1, detectCores() - 2),
  verbose = FALSE,
  ...
)

Arguments

event

a surf object.

sampleData

data.frame, must contain two columns – "bam" and "condition" (for "IP" and "input", where "IP" should come first), whose row.names represent the sample names. "bam" is the file name of CLIP-seq bam. "condition" will be coerced to factor, whose first level will be treated as IP, and the second level as input.

signal.type

character, indicate the type of feature signal wanted, support "TPM" for Transcripts Per Kilobase Million, "FPKM" for Fragments Per Kilobase Million (for paired-end reads) and Reads Per Kilobase Million (for single-end reads), and "raw.count" for raw read counts

FUN.aggregate

function, used for aggregating signals within condition, default to mean().

minMQS, minOverlap, isPairedEnd, ...

parameters for featureCounts. minMQS is default to 10, and minOverlap is default to 12 (25% of the typical read length of CLIP-seq (~50bp)), and isPairedEnd is default to TRUE.

cores

integer, number of available workers, sent to nthreads of featureCounts

verbose

logical, whether (default to TRUE) to echo progress

Details

If your sequencing platform is Illumina HiSeq 2000, set strandSpecific = 2.

Value

a surf object, with (1) one column featureSignal added, (2) faseqData slot updated, and (3) sampleData slot updated.

References

https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/


fchen365/surf documentation built on June 18, 2021, 12:02 p.m.