## ----knitr_opts, echo = FALSE-------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center"
)

## ----init, echo = FALSE, message = FALSE--------------------------------------
library(valr)
library(dplyr)
library(ggplot2)
library(tibble)

## ----syntax_demo, message = FALSE---------------------------------------------
library(valr)
library(dplyr)

snps <- read_bed(valr_example('hg19.snps147.chr22.bed.gz'), n_fields = 6)
genes <- read_bed(valr_example('genes.hg19.chr22.bed.gz'), n_fields = 6)

# find snps in intergenic regions
intergenic <- bed_subtract(snps, genes)
# distance from intergenic snps to nearest gene
nearby <- bed_closest(intergenic, genes)

nearby %>%
  select(starts_with('name'), .overlap, .dist) %>%
  filter(abs(.dist) < 1000)

## ----file_io------------------------------------------------------------------
bed_file <- valr_example("3fields.bed.gz")
read_bed(bed_file) # accepts filepaths or URLs

## ----trbl_ivls----------------------------------------------------------------
bed <- tribble(
  ~chrom, ~start,  ~end, 
  "chr1", 1657492, 2657492, 
  "chr2", 2501324, 3094650
)

bed

## ----zero-based---------------------------------------------------------------
# a chromosome 100 basepairs in length
chrom <- tribble(
  ~chrom, ~start, ~end, 
  "chr1", 0,      100
)

chrom

# single basepair intervals
bases <- tribble(
  ~chrom, ~start, ~end, 
  "chr1", 0,      1, # first base of chromosome
  "chr1", 1,      2,  # second base of chromosome
  "chr1", 99,     100 # last base of chromosome
)

bases

## ----db, warning = FALSE, eval = FALSE----------------------------------------
#  # access the `refGene` tbl on the `hg38` assembly.
#  if(require(RMySQL)) {
#    ucsc <- db_ucsc('hg38')
#    tbl(ucsc, 'refGene')
#  }

## ----intersect_glyph----------------------------------------------------------
x <- tribble(
  ~chrom, ~start, ~end,
  'chr1', 25,     50,
  'chr1', 100,    125
)

y <- tribble(
  ~chrom, ~start, ~end,
  'chr1', 30,     75
)

bed_glyph(bed_intersect(x, y))

## ----merge_glyph--------------------------------------------------------------
x <- tribble(
  ~chrom, ~start, ~end,
  'chr1',      1,      50,
  'chr1',      10,     75,
  'chr1',      100,    120
)

bed_glyph(bed_merge(x))

## ----strand-------------------------------------------------------------------
x <- tribble(
  ~chrom, ~start, ~end, ~strand,
  'chr1', 1,      100,  '+',
  'chr1', 50,     150,  '+',
  'chr2', 100,    200,  '-'
)

y <- tribble(
  ~chrom, ~start, ~end, ~strand,
  'chr1', 50,     125,  '+',
  'chr1', 50,     150,  '-',
  'chr2', 50,     150,  '+'
)

# intersect tbls by strand
x <- group_by(x, strand)
y <- group_by(y, strand)

bed_intersect(x, y)

## ----strand_opp---------------------------------------------------------------
x <- group_by(x, strand)

y <- flip_strands(y)
y <- group_by(y, strand)

bed_intersect(x, y)

## ----NSE, eval = FALSE--------------------------------------------------------
#  # calculate the mean and variance for a `value` column
#  bed_map(a, b, .mean = mean(value), .var = var(value))
#  
#  # report concatenated and max values for merged intervals
#  bed_merge(a, .concat = concat(value), .max = max(value))

## ----demo-tss, warning = FALSE, message = FALSE-------------------------------
# `valr_example()` identifies the path of example files
bedfile <- valr_example('genes.hg19.chr22.bed.gz')
genomefile <- valr_example('hg19.chrom.sizes.gz')
bgfile  <- valr_example('hela.h3k4.chip.bg.gz')

genes <- read_bed(bedfile, n_fields = 6)
genome <- read_genome(genomefile)
y <- read_bedgraph(bgfile)

## ----tss----------------------------------------------------------------------
# generate 1 bp TSS intervals, `+` strand only
tss <- genes %>%
  filter(strand == '+') %>%
  mutate(end = start + 1)

# 1000 bp up and downstream
region_size <- 1000
# 50 bp windows
win_size <- 50

# add slop to the TSS, break into windows and add a group
x <- tss %>%
  bed_slop(genome, both = region_size) %>%
  bed_makewindows(win_size)

x

## ----map----------------------------------------------------------------------
# map signals to TSS regions and calculate summary statistics.
res <- bed_map(x, y, win_sum = sum(value, na.rm = TRUE)) %>%
  group_by(.win_id) %>%
  summarize(win_mean = mean(win_sum, na.rm = TRUE),
            win_sd = sd(win_sum, na.rm = TRUE))

res

## ----plot, warning = FALSE, message = FALSE, fig.align='center', fig.width=6----
library(ggplot2)

x_labels <- seq(-region_size, region_size, by = win_size * 5)
x_breaks <- seq(1, 41, by = 5)

sd_limits <- aes(ymax = win_mean + win_sd, ymin = win_mean - win_sd)

ggplot(res, aes(x = .win_id, y = win_mean)) +
  geom_point() + geom_pointrange(sd_limits) + 
  scale_x_continuous(labels = x_labels, breaks = x_breaks) + 
  xlab('Position (bp from TSS)') + ylab('Signal') + 
  ggtitle('Human H3K4me3 signal near transcription start sites') +
  theme_classic()

