Man pages for exomePeak2
Bias Awared Peak Calling and Quantification for MeRIP-Seq
| call_peaks_with_GLM | Statistical Inference with DESeq package based on the... |
| consDESeq2_DM | Calculate the index for across sample differential... |
| consDESeq2_M | Calculate the index for across sample modification... |
| convertTxDb | Convert the txdb object into the full transcript and whole... |
| ctest | Exact poisson test on the ratio between IP and input counts. |
| decision_deseq2 | Calculate the decision table for a DESeq2 result. |
| disj_background | Find the background of the user provided mod_gration. |
| estimateSeqDepth-methods | Method estimateSeqDepth |
| exome_bins_from_txdb | extract exome bins for peak calling given a txdb object |
| exomePeak2 | Peak Calling and Peak Statistics Quantification on MeRIP-seq... |
| exomePeak2Results-methods | Method exomePeak2Results |
| exomePeakCalling-methods | Method exomePeakCalling |
| ExonPlot | plot the distribution for the length of the overlapped exons. |
| exons_by_unique_gene | Extracting exons by the corresponding genes that are on the... |
| exportResults-methods | Method exportResults |
| flank_on_exons | Flank ranges on exon coordinate. |
| GC_content_over_grl | Retrieve GC content level from genome over regions defined by... |
| GCsizeFactors-methods | Method GCsizeFactors |
| glmDM-methods | Method glmDM |
| GLM_inference | Statistical Inference with DESeq2 on IP over input fold... |
| glmM-methods | Method glmM |
| LibraryType-methods | Method LibraryType |
| mclust_bg | Find background of merip-seq signal with model based... |
| MeripBamFileList-class | Maintain and use BAM files in MeRIP-Seq experiment |
| normalizeGC-methods | Method normalizeGC |
| Parameter-methods | Method Parameter |
| plotExonLength-methods | Method plotExonLength |
| plotLfcGC-methods | Method plotLfcGC |
| plotReadsGC-methods | Method plotReadsGC |
| plotSizeFactors-methods | Method plotSizeFactors |
| quiet | Silencing unwanted function output. |
| reads_five_POS | extract reads five prime POS. |
| reads_five_POS_rev | extract reads five prime POS and reverse its strand. |
| reduce_peaks | A function to reduce ranges between elements within a... |
| remove_introns | Removing introns from a provided GRanges object. |
| replace_bg | Replace the control regions with user provided background. |
| Results-methods | Method Results |
| scanMeripBAM | Organize the BAM Files Information of a MeRIP-seq Data Set. |
| split_by_name | a function to split a GRanges into GRangesList by its names. |
| SummarizedExomePeak-class | SummarizedExomePeak |
