scanMeripBAM {exomePeak2} | R Documentation |
scanMeripBAM
check and organize the BAM files in MeRIP-seq data before peak calling using exomePeakCalling
.
The library types of the RNA-seq and the filters such as SAM FLAG score are specified in this function.
scanMeripBAM( bam_ip = NULL, bam_input = NULL, bam_treated_ip = NULL, bam_treated_input = NULL, paired_end = FALSE, library_type = c("unstranded", "1st_strand", "2nd_strand"), index_bam = TRUE, bam_files = NULL, design_ip = NULL, design_treatment = NULL, mapq = 30L, isSecondaryAlignment = FALSE, isNotPassingQualityControls = FALSE, isDuplicate = FALSE, isPaired = NA, isProperPair = NA, hasUnmappedMate = NA, ... )
bam_ip |
a |
bam_input |
a |
bam_treated_ip |
a |
bam_treated_input |
a If the bam files do not contain treatment group, user should only fill the arguments of |
paired_end |
a |
library_type |
a
|
index_bam |
a The BAM index files will be named by adding ".bai" after the names of the corresponding BAM files. |
bam_files |
optional, a |
design_ip |
optional, a |
design_treatment |
optional, a |
mapq |
a non-negative integer specifying the minimum reads mapping quality. BAM records with mapping qualities less than |
isPaired, isProperPair, hasUnmappedMate, isSecondaryAlignment, isNotPassingQualityControls, isDuplicate, ... |
arguments specifying the filters on SAM FLAG scores, inherited from |
scanMeripBAM
takes the input of the BAM file directories for the MeRIP-seq datasets.
It first checks the completeness of the BAM files and the BAM indexes. Then, the design information of IP/input and treated/control are returned as a MeripBamFileList
object.
If the BAM file indexes are missing, the BAM files will be automatically indexed with the package Rsamtools
.
a MeripBamFileList
object.
### Define BAM File Directories f1 = system.file("extdata", "IP1.bam", package="exomePeak2") f2 = system.file("extdata", "IP2.bam", package="exomePeak2") f3 = system.file("extdata", "IP3.bam", package="exomePeak2") f4 = system.file("extdata", "IP4.bam", package="exomePeak2") IP_BAM = c(f1,f2,f3,f4) f1 = system.file("extdata", "Input1.bam", package="exomePeak2") f2 = system.file("extdata", "Input2.bam", package="exomePeak2") f3 = system.file("extdata", "Input3.bam", package="exomePeak2") INPUT_BAM = c(f1,f2,f3) f1 = system.file("extdata", "treated_IP1.bam", package="exomePeak2") TREATED_IP_BAM = c(f1) f1 = system.file("extdata", "treated_Input1.bam", package="exomePeak2") TREATED_INPUT_BAM = c(f1) ### For MeRIP-Seq Experiment Without the Treatment Group MeRIP_Seq_Alignment <- scanMeripBAM( bam_ip = IP_BAM, bam_input = INPUT_BAM, paired_end = FALSE ) ### For MeRIP-Seq Experiment With the Treatment Group MeRIP_Seq_Alignment <- scanMeripBAM( bam_ip = IP_BAM, bam_input = INPUT_BAM, bam_treated_ip = TREATED_IP_BAM, bam_treated_input = TREATED_INPUT_BAM, paired_end = FALSE )