Integrating Cap Enrichment with Transcript Expression Analysis


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Documentation for package ‘icetea’ version 1.27.0

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activeChrs Match BAM headers bw files and get active chromosome list (from restrict) (written by Aaron Lun, 12 Dec 2014, copied and modified here)
annotateTSS Annotate the provided Transcription Start Sites
CapSet Create a new CapSet object
CapSet-class Create a new CapSet object
check_capSet Check capset validity
demultiplexFASTQ Demultiplex and tag fastq files using sample barcodes
demultiplexFASTQ-method Demultiplex and tag fastq files using sample barcodes
detectDiffTSS Detect differentially expressed Transcription Start Sites between two conditions (test)
detectDiffTSS-method Detect differentially expressed Transcription Start Sites between two conditions (test)
detectTSS Detection of Trancription start sites based on local enrichment
detectTSS-method Detection of Trancription start sites based on local enrichment
diffQCplots Make DESeq2 or edgeR QC plots
exampleCSobject Create example CapSet object
exportTSS Export the detected TSS from CapSet object as .bed files
exportTSS-method Export the detected TSS from CapSet object as .bed files
filterDuplicates Filter PCR-duplicates from mapped files using internal UMIs
filterDuplicates-method Filter PCR-duplicates from mapped files using internal UMIs
filterDups Filter PCR-duplicates from BAM file using internal UMIs
fitDiffTSS Detect differentially expressed Transcription Start Sites between two conditions (fit model)
fitDiffTSS-method Detect differentially expressed Transcription Start Sites between two conditions (fit model)
getBamFlags Get flags to read from bam
getChromBins Get chromosome bins from BAM files
getChromWindows Get chromosome sliding windows from BAM files
getGeneCounts Get gene-level counts from TSS data
getGeneCounts-method Get gene-level counts from TSS data
getMCparams Get platform-specific multicore params
getNormFactors Calculate normalization factors from CapSet object
getNormFactors-method Calculate normalization factors from CapSet object
getranks Assign feature ranks on a VariantAnnotation output
get_newfastq Get data to create new ShortReadQ object after barcode trimming
mapCaps Map the data from 5' profiling techniques
mapCaps-method Map the data from 5' profiling techniques
newCapSet Create a new CapSet object
numReadsInBed Count the number of reads in a given GRanges
plotPrecision Plotprecision background script
plotReadStats Plot read statistics from the CapSet object
plotReadStats-method Plot read statistics from the CapSet object
plotTSSprecision Compare the precision of TSS detection between multiple samples
plotTSSprecision-method Compare the precision of TSS detection between multiple samples
readsTo3p preprocess reads to count only 3' overlaps
readsTo5p preprocess reads to count only 5' overlaps
readsToCenter preprocess reads to count only center overlaps
sampleInfo Retrieve and replace sample information of a CapSet object
sampleInfo-method Retrieve and replace sample information of a CapSet object
sampleInfo<- Retrieve and replace sample information of a CapSet object
sampleInfo<--method Retrieve and replace sample information of a CapSet object
splitBAM_byIndex Split the composite BAM file using internal indexes (MAPCap)
splitBAM_byRepindex Split the composite BAM file using replicate indexes (MAPCap data)
splitranks Get features with the best rank for each TSS
split_fastq Split paired-end fastq by barcodes
strandBinCounts Perform stranded Bin counts