faseqCount: Construct FASeq Data Set
In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description Usage Arguments Details Value References

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.

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

`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