getPermutatedWinScores {CSAR} | R Documentation |
Obtain the read-enrichment score distribution under the null hypothesis
getPermutatedWinScores(file, nn)
file |
Name of the file generated by permutatedWinScores |
nn |
ID for the multiple permutation process |
Numeric vector of score values under permutation
Jose M Muino, jose.muino@wur.nl
Muino et al. (submitted). Plant ChIP-seq Analyzer: An R package for the statistcal detection of protein-bound genomic regions.
Kaufmann et al.(2009).Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biology; 7(4):e1000090.
CSAR-package, permutatedWinScores
##For this example we will use the a subset of the SEP3 ChIP-seq data (Kaufmann, 2009) data("CSAR-dataset"); ##We calculate the number of hits for each nucleotide posotion for the control and sample. We do that just for chromosome chr1, and for positions 1 to 10kb nhitsS<-mappedReads2Nhits(sampleSEP3_test,file="sampleSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000)) nhitsC<-mappedReads2Nhits(controlSEP3_test,file="controlSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000)) ##We calculate two sets of read-enrichment scores through permutation permutatedWinScores(nn=1,sample=sampleSEP3_test,control=controlSEP3_test,fileOutput="test",chr=c("CHR1v01212004"),chrL=c(100000)) permutatedWinScores(nn=2,sample=sampleSEP3_test,control=controlSEP3_test,fileOutput="test",chr=c("CHR1v01212004"),chrL=c(100000)) ###Next function will get all permutated score values generated by permutatedWinScores function. ##This represent the score distribution under the null hypotesis and therefore it can be use to control the error of our test. nulldist<-getPermutatedWinScores(file="test",nn=1:2)