PeptideDisplayPipe: The analysis pipeline of peptide display data

In WubingZhang/PhageR: Functions for phage display data analysis

Description

The analysis pipeline of peptide display data

Usage

PeptideDisplayPipe(fastqs = NULL, rawcount = NULL, proj = "Peptide",
  outdir = "./", pwAlignRes = NULL,
  pwAlignRDS = "Bacterial_Display_Mmu.rds", top = 1000,
  topnames = c("PDCD1", "CTLA4", "PD1L1", "PD1L2"), ctl = 1, trt = 2,
  peplen = 12, distrAA = FALSE, nperm = 30, core = 2,
  refseq_fa = "~/Jobs/Project/XunBaihui/_Data/6_PhageDisplay/Mmu_Proteosome/UP000000589_10090.fasta")

Arguments

fastqs	A vector of path to fastq files.
rawcount	Raw count matrix.
proj	Character, can be the experiment name.
outdir	The path to output directory.
pwAlignRes	A data frame.
pwAlignRDS	The path to pairwise alignment dictionary.
top	Integer, specifying the number of top peptides to be selected.
topnames	A vector of proteins to be labeled.
ctl	Index of controls.
trt	Index of treatments.
peplen	The length of peptides in the library.
distrAA	Boolean, indicating whether test the distribution of AA in peptides.
nperm	The permutation time.
core	The number of core to use.
refseq_fa	The path to refseq fasta file.

Author(s)

Wubing Zhang

Examples

setwd("~/Jobs/Project/XunBaihui/_Data/6_PhageDisplay/20190124/")
ctl_fq = "fastq/s20190124-XBH-42_TB_patient1_1st.fq.gz"
trt_fq = "fastq/s20190124-XBH-65_TB_patient1_3rd.fq.gz"
proj = "Patient1"
outdir = "./"
PeptideDisplayPipe(c(ctl_fq, trt_fq), proj=proj)

WubingZhang/PhageR documentation built on July 2, 2019, 9:03 p.m.