We can make this file beautiful and searchable if this error is corrected: It looks like row 6 should actually have 28 columns, instead of 7. in line 5.
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Index CHR,Index SNP,BP Left,BP Right,# Conditional independent,Index BP,Index P value,Merged Indexes,2nd SNP,2nd BP,2nd P value,3rd SNP,3rd BP,3rd P value,4th SNP,4th BP,4th P value,5th SNP,5th BP,5th P value,,,,,,,, | |
6,rs13195636,24939493,30559493,4,27509493,3.33E-40,rs13195636,rs9461856,33395199,4.13E-14,rs8192589,32187637,2.27E-10,rs9368789,34001678,2.03E-07,rs10946808,26233387,1.11E-06,,,,,,,, | |
18,rs9636107,52666708,53680258,4,53200117,1.92E-13,"rs12969453,rs74914300,rs72934602,rs9636107",rs12969453,52751708,3.93E-11,rs78322266,53063676,6.89E-08,rs72934602,53568458,6.79E-07,rs9952704,53447690,2.60E-04,,,,,,,, | |
3,rs2710323,48132866,53603354,3,52815905,1.02E-21,"rs11715134,rs11917680,rs2710323,rs13080668",rs2236989,50505395,1.81E-10,rs7633840,48719638,4.41E-07,rs4687724,53408177,1.10E-04,,,,,,,,,,, | |
18,rs72980087,77324421,77981194,2,77632194,4.80E-16,"rs56040937,rs7238071,rs72980087,rs72970145",rs11664298,77578986,5.24E-16,rs12455965,77688830,0.0001109,,,,,,,,,,,,,, | |
3,rs13090130,161092491,161969035,2,161777035, |
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library(plyranges) | |
x <- data.frame(seqnames=1, | |
start=sample(1000,10,FALSE), | |
width=1, id=1:10) %>% | |
as_granges() | |
y <- data.frame(seqnames=1, | |
start=sample(1000,10,FALSE), | |
width=1, id=letters[1:10]) %>% | |
as_granges() |
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library(plyranges) | |
library(microbenchmark) | |
library(dplyr) | |
library(tibble) | |
make_rand_gr <- function(N, grps) { | |
data.frame(seqnames = sample(c("seq1", "seq2", "seq3"), N, replace = TRUE), | |
strand = sample(c("+", "-", "*"), N, replace = TRUE), start = rpois(N, | |
N), width = rpois(N, N), grps = sample(grps, N, replace = TRUE), | |
score = runif(N)) %>% as_granges() |
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airway@assays@data[["counts"]][airway@rowRanges@elementMetadata@listData$gene_id == "ENSG00000000003", airway@colData@listData$dex == "trt"] | |
assays(airway)[["counts"]][names(rowRanges(airway)) == "ENSG00000000003", colData(airway)$dex == "trt"] | |
assay(airway, "counts")["ENSG00000000003", airway$dex == "trt"] | |
airway |> filter(symbol == "TSPAN6", dex == "trt") |> pull(counts) |
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# scraped from https://doi.org/10.1038/nature11241 | |
# note that intersections < 100 not included | |
banana_sets <- c( | |
Musa = 759, | |
Phoenix = 769, | |
Sorghum = 827, | |
Brachypodium = 387, | |
Ozyza = 1246, | |
Arabidopsis = 1187, | |
`Musa&Phoenix` = 467, |
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library(plyranges) | |
set.seed(1) | |
x <- data.frame(seqnames=1, start=0:9 * 100 + 1, | |
width=20, id=1:10) %>% | |
as_granges() | |
y <- data.frame(seqnames=1, start=round(runif(4,100,900)), | |
width=10, id=letters[1:4]) %>% | |
as_granges() %>% |
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library(splines) | |
library(DESeq2) | |
# make some demo data | |
dds <- makeExampleDESeqDataSet(n=100, m=40) | |
dds$condition <- sort(runif(40)) | |
# make one gene where expression has a curve shape (just for demo) | |
s_shape <- round(500 * sin(dds$condition*2*pi) + 1000 + rnorm(40,0,50)) | |
mode(s_shape) <- "integer" | |
counts(dds)[1,] <- s_shape |
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library(tm) | |
library(wordcloud) | |
crude <- scan("words", what="char", sep="\n") | |
crude <- gsub("/"," ",crude) | |
crude <- gsub("single cell","singlecell",crude) | |
crude <- Corpus(VectorSource(crude)) | |
crude <- suppressWarnings(tm_map(crude, removePunctuation)) | |
crude <- suppressWarnings(tm_map(crude, function(x) removeWords(x, stopwords()))) | |
tdm <- TermDocumentMatrix(crude) | |
m <- as.matrix(tdm) |
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design <- ~0 + donor + allele | |
dds <- DESeqDataSetFromMatrix(counts, coldata, design) # counts has the two alleles per donor | |
assays(dds)[["weights"]] <- weights # 1 for hets, 1e-6 for homs | |
sizeFactors(dds) <- rep(1, ncol(dds)) | |
dds <- DESeq(dds, test="LRT", reduced=~0 + donor) | |
res <- results(dds) |
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library(plotgardener) | |
par <- pgParams( | |
chrom = "chr1", | |
chromstart = 8.2e6, | |
chromend = 8.7e6, | |
assembly = "hg19", | |
just = c("left", "bottom") | |
) | |
dat <- data.frame(chrom="chr1", pos=840:849 * 1e4 + 1, p=1:10/10) | |
pageCreate(width = 4, height = 3.5, showGuides = TRUE) |