Description Usage Arguments Value Examples
Generate precision recall curve and related statistics directly from bam files.
1 2 3 4 5 6 7 8 9 10 11 | OneStep_PRC(
bam_ip,
bam_input,
txdb,
bsgenome = NULL,
paired_end = FALSE,
ground_truce_gr,
exp_label = "MeRIP_experiment_1",
N = 200,
glm_type = "DESeq2"
)
|
bam_ip |
a vector containing the BAM files for IP samples. |
bam_input |
a vector containing the BAM files for input samples. |
txdb |
a TxDb object for the transcript annotation. |
bsgenome |
a BSgenome object for the genome sequence. |
paired_end |
a logical value indicating wheather the data is paired end sequencing; default = FALSE. |
ground_truce_gr |
a GRanges for the ground truce of positive methylation sites, recommended to be in single based resolution. |
exp_label |
a character for the label of the experiment; default = "MeRIP_experiment_1". |
N |
number of points sampled for each PRC curve; default = 200. |
glm_type |
type of GLM fit when peak calling; default = "DESeq2". |
The table for AUPRC and the AUROC curve will be saved on the disc under a folder named by exp_label.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | library(exomePeak2Test)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(exomePeak2)
library(BSgenome.Hsapiens.UCSC.hg19)
whistle_predict <- readRDS("predictedResults.rds")
whistle_gr <- readRDS("exon_DRACH.rds")
whistle_gr$prob <- whistle_predict
OneStep_PRC(bam_ip = c("bam_local/SRR1035214_sorted.bam",
"bam_local/SRR1035216_sorted.bam",
"bam_local/SRR1035222_sorted.bam",
"bam_local/SRR1035224_sorted.bam"),
bam_input = c("bam_local/SRR1035213_sorted.bam",
"bam_local/SRR1035215_sorted.bam",
"bam_local/SRR1035221_sorted.bam",
"bam_local/SRR1035223_sorted.bam"),
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
bsgenome = Hsapiens,
paired_end = FALSE,
ground_truce_gr = whistle_gr[whistle_gr$prob > 0.5],
exp_label = "MeRIP_experiment_1",
N = 200)
|
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