매칭 및 필터링

R로 시작하는 Bioconductor

Paula Andrea Martinez, PhD.

Data Scientist

중복 서열

자연계에서 발생하는 생물학적 서열 중복
라이브러리 제작 단계(PCR)에서의 증폭
동일 샘플의 반복 시퀀싱

중복 제거 또는 표시

전장 유전체 시퀀싱 또는 엑솜 시퀀싱

임계값을 이용한 중복 표시

RNA-seq 및 ChIP-seq

srduplicated

library(ShortRead)

# Counting duplicates TRUE is the number of duplicates
table(srduplicated(dfqsample))

FALSE  TRUE 
500   500

# Cleaning reads from duplicates x[fun(x)]
cleanReads <- mydReads[srduplicated(mydReads) == FALSE]

# Counting duplicates
table(srduplicated(cleanReads))

FALSE
500

사용자 정의 필터 만들기

srFilter로 조건 기반 필터링 x[fun(x)]

필터 예시

library(ShortRead)

# Use a custom filter to remove reads from fqsample
# This filter to remove reads shorter than a min number of bases
readWidthCutOff <- srFilter(function(x) {width(x) >= minWidth}, 
                            name = "MinWidth")

minWidth <- 51

fqsample[readWidthCutOff(fqsample)]

nFilter

library(ShortRead)

# save your filter, .name is optional
myFilter <- nFilter(threshold = 10, .name = "cleanNFilter")

# use the filter at reading point    
filtered <- readFastq(dirPath = "data", 
                      pattern = ".fastq",
                       filter = myFilter)

# you will retrieve only those reads that have a maximum of 10 N's
filtered

idFilter와 polynFilter

library(ShortRead)

#id filter example
myFilterID <- idFilter(regex = ":3:1")
# will return only those ids that contain the regular expression

# optional parameters are .name, fixed and exclude
# use the filter at reading point    
filtered <- readFastq(dirPath = "data", pattern = ".fastq",
                       filter = myFilterID)

# filter to remove poly-A regions
myFilterPolyA <- polynFilter(threshold = 10, nuc = c("A"))
# will return the sequences that have a maximun number of 10 consecutive A's

# use the filter for subsetting    
filtered[myFilterPolyA(filtered)]

필터 사용 연습!

R로 시작하는 Bioconductor