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July 17, 2017 23:37
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# Section 1 | |
library("Bioc2017.TCGAbiolinks.ELMER") | |
library(TCGAbiolinks) | |
library(SummarizedExperiment) | |
library(DT) | |
library(dplyr) | |
query.exp <- GDCquery(project = "TCGA-LUSC", | |
data.category = "Transcriptome Profiling", | |
data.type = "Gene Expression Quantification", | |
workflow.type = "HTSeq - FPKM-UQ", | |
barcode = c("TCGA-34-5231-01","TCGA-77-7138-01")) | |
GDCdownload(query.exp) | |
exp <- GDCprepare(query = query.exp, | |
save = TRUE, | |
save.filename = "Exp_LUSC.rda", | |
summarizedExperiment = TRUE) | |
query.met <- GDCquery(project = "TCGA-LUSC", | |
data.category = "DNA Methylation", | |
platform = "Illumina Human Methylation 450", | |
barcode = c("TCGA-34-5231-01A-21D-1818-05","TCGA-77-7138-01A-41D-2043-05")) | |
GDCdownload(query.met) | |
met <- GDCprepare(query = query.met, | |
save = TRUE, | |
save.filename = "DNAmethylation_LUSC.rda", | |
summarizedExperiment = TRUE) | |
# Section 2 | |
library("Bioc2017.TCGAbiolinks.ELMER") | |
library(MultiAssayExperiment) | |
library(ELMER) | |
lusc.exp | |
lusc.met | |
distal.probes <- get.feature.probe(genome = "hg38", met.platform = "450K") | |
mae <- createMAE(exp = lusc.exp, | |
met = lusc.met, | |
save = TRUE, | |
linearize.exp = TRUE, | |
filter.probes = distal.probes, | |
save.filename = "mae_bioc2017.rda", | |
met.platform = "450K", | |
genome = "hg19", | |
TCGA = TRUE) | |
mae | |
colData(mae)[1:5,] %>% as.data.frame %>% datatable(options = list(scrollX = TRUE)) | |
sampleMap(mae)[1:5,] %>% as.data.frame %>% datatable(options = list(scrollX = TRUE)) | |
sig.diff <- get.diff.meth(data = mae, | |
group.col = "definition", | |
group1 = "Primary solid Tumor", | |
group2 = "Solid Tissue Normal", | |
minSubgroupFrac = 0.2, | |
sig.dif = 0.3, | |
diff.dir = "hypo", # Search for hypomethylated probes in group 1 | |
cores = 1, | |
dir.out ="result", | |
pvalue = 0.01) | |
nearGenes <- GetNearGenes(data = mae, | |
probes = sig.diff$probe, | |
numFlankingGenes = 20, # 10 upstream and 10 dowstream genes | |
cores = 1) | |
Hypo.pair <- get.pair(data = mae, | |
group.col = "definition", | |
group1 = "Primary solid Tumor", | |
group2 = "Solid Tissue Normal", | |
nearGenes = nearGenes, | |
minSubgroupFrac = 0.4, # % of samples to use in to create groups U/M | |
permu.dir = "result/permu", | |
permu.size = 100, # Please set to 100000 to get significant results | |
pvalue = 0.05, | |
Pe = 0.01, # Please set to 0.001 to get significant results | |
filter.probes = TRUE, # See preAssociationProbeFiltering function | |
filter.percentage = 0.05, | |
filter.portion = 0.3, | |
dir.out = "result", | |
cores = 1, | |
label = "hypo") | |
enriched.motif <- get.enriched.motif(data = mae, | |
probes = Hypo.pair$Probe, | |
dir.out = "result", | |
label = "hypo", | |
min.incidence = 10, | |
lower.OR = 1.1) | |
names(enriched.motif) # enriched motifs | |
head(enriched.motif["P73_HUMAN.H10MO.A"]) ## probes in the given set that have TP53 motif. | |
## identify regulatory TF for the enriched motifs | |
TF <- get.TFs(data = mae, | |
group.col = "definition", | |
group1 = "Primary solid Tumor", | |
group2 = "Solid Tissue Normal", | |
minSubgroupFrac = 0.4, | |
enriched.motif = enriched.motif, | |
dir.out = "result", | |
cores = 1, | |
label = "hypo") |
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