farris_sashimi_files_df: Sashimi plot files data.frame for Farris data

In jmw86069/farrisdata: Farris et al Mouse Hippocampus RNA-seq data objects

Description

Sashimi plot files data.frame for Farris data

Usage

farris_sashimi_files_df

Format

data.frame suitable for use with splicejam::prepareSashimi() for the filesDF argument.

Examples

#farris_sashimi_files_df
base_url <- "https://orio.niehs.nih.gov/ucscview/farrisHub/mm10/";
factor1 <- c("CA1", "CA2", "CA3", "DG");
factor2 <- c("CB", "DE");
junc_suffix <- ".STAR_mm10.combinedJunctions.bed.gz";
junc_urls <- paste0(base_url,
   rep(factor1, each=2),
   "_",
   rep(factor2, 4),
   junc_suffix);
junc_sample_id <- paste(rep(factor1, each=2),
   rep(factor2, 4),
   sep="_");
junc_scale_factors <- 2^c(
   CA1_CB=-0.185,
   CA1_DE=0.146,
   CA2_CB=-0.241,
   CA2_DE=0.765,
   CA3_CB=-0.215,
   CA3_DE=0.256,
   DG_CB=-0.376,
   DG_DE=0.372);
junc_df <- data.frame(sample_id=junc_sample_id,
   url=junc_urls,
   type="junction",
   scale_factor=junc_scale_factors[junc_sample_id]);
if (suppressPackageStartupMessages(require(knitr))) {
   knitr::kable(junc_df)
} else {
   junc_df;
}

bw_factor1 <- c(factor1);
bw_factor2 <- c(factor2);
bw_base_url <- paste0(base_url, "union_bigwig/");
bw_strand <- c("pos", "neg");
bw_suffix <- ".bw";
bw_urls <- paste0(
   rep(bw_factor1, each=4),
   "_",
   rep(bw_factor2, each=2),
   ".union.",
   bw_strand,
   bw_suffix
);
bw_scale_factors <- 2^c(
   CA1_CB=-0.0157,
   CA1_DE=0.306,
   CA2_CB=-0.0266,
   CA2_DE=0.0947,
   CA3_CB=0.00839,
   CA3_DE=0.528,
   DG_CB=-0.243,
   DG_DE=-0.283);

if (suppressPackageStartupMessages(require(knitr))) {
   knitr::kable(as.data.frame(matrix(bw_urls, ncol=5)))
} else {
   as.data.frame(matrix(bw_urls, ncol=4));
}

# remove NA entries
bw_url <- jamba::rmNA(bw_urls);
bw_sample_id <- gsub("^.*(CA[123]|DG)[_]*(CB|DE).*",
   "\\1_\\2",
   bw_url);
bw_df <- data.frame(
   url=paste0(bw_base_url, bw_url),
   sample_id=bw_sample_id,
   type="bw",
   scale_factor=bw_scale_factors[bw_sample_id]);
bw_df <- bw_df[do.call(order, bw_df[,c(2,1,3)]),];

farris_sashimi_files_df <- rbind(
   junc_df,
   bw_df);
# replace missing scale_factor with 1, should not be necessary
farris_sashimi_files_df$scale_factor[is.na(farris_sashimi_files_df$scale_factor)] <- 1;
farris_sashimi_files_df$CellType <- factor(
   gsub("_.+", "",
      farris_sashimi_files_df$sample_id),
   levels=factor1);
farris_sashimi_files_df$Compartment <- factor(
   gsub("^.+_", "",
      farris_sashimi_files_df$sample_id),
   levels=factor2);
if (suppressPackageStartupMessages(require(knitr))) {
   knitr::kable(farris_sashimi_files_df)
} else {
   farris_sashimi_files_df;
}

table(farris_sashimi_files_df[,c("CellType", "Compartment", "type")]);

jmw86069/farrisdata documentation built on Oct. 8, 2019, 9:56 p.m.