Errata and updates for Chapter 8 #19
Description
(Page 181)
You access access R’s built-in documentation
should be
You access R’s built-in documentation
(Page 181)
apropos(norm)
printed "Error: is.character(what) is not TRUE", and thus should be
apropos("norm")
(Page 197)
(or use asis;
should be
(or use as.is;
(Page 202)
by dd$start >= 25800000 and dd$end <= 29700000 and
should be
by d$start >= 25800000 and d$end <= 29700000 and
(Page 205)
because d$percent is a vector,
should be
because d$percent.GC is a vector,
(Page 206)
Thus, d[$Pi > 3, ] is identical to d[which(d$Pi > 3), ];
should be
Thus, d[d$Pi > 3, ] is identical to d[which(d$Pi > 3), ];
(Page 208)
gplot2’s grammar through examples.
should be
ggplot2’s grammar through examples.
Page 218
Finding the Right Bin Width
ggplot(d) + geom_bar(aes(x=Pi), binwidth=1) + scale_x_continuous(limits=c(0.01, 80))
printed the following Warning messages:
## Warning: Ignoring unknown parameters: binwidth
## Warning: Removed 3373 rows containing non-finite values (stat_count).
Page 211
—everything is saturated from about 0.05 and below.
should be
—everything is saturated from about 0.005 and below.
(Page 216)
a factor (e.g., d$binned.GC)
should be
a factor (e.g., d$GC.binned)
(Page 217)
Total.SNPs,
should be
total.SNPs,
(Page 219)
try class(d$repClass) and levels(d$repClass)
should be
try class(reps$repClass) and levels(reps$repClass)
Page 222
The pos column is already present in
https://raw.githubusercontent.com/vsbuffalo/bds-files/master/chapter-08-r/motif_recombrates.txt
> mtfs <- read.delim("motif_recombrates.txt", header=TRUE, stringsAsFactors=TRUE)
> head(mtfs, 3)
chr motif_start motif_end dist recomb_start recomb_end recom
1 chrX 35471312 35471325 39323.0 35430651 35433340 0.0015
2 chrX 35471312 35471325 36977.0 35433339 35435344 0.0015
3 chrX 35471312 35471325 34797.5 35435343 35437699 0.0015
motif pos
1 CCTCCCTGACCAC chrX-35471312
2 CCTCCCTGACCAC chrX-35471312
3 CCTCCCTGACCAC chrX-35471312
(Page 231)
> set.seed(0) # we set the random number seed so this example is reproducible
should be added before
> ll <- list(a=rnorm(6, mean=1), b=rnorm(6, mean=4), c=rnorm(6, mean=6))
Page 232
> lapply(ll, mean)
$a
[1] 0.5103648
$b
[1] 0.09681026
$c
[1] -0.2847329
should be
> lapply(ll, mean)
$a
[1] 1.402273
$b
[1] 4.19003
$c
[1] 5.53541
(Page 244)
*My output was
not the order "position GC.binned diversity" as shown in the book
but the order "diversity position GC.binned" as shown below: *
> select(d_df, -(start:cent))
Source: local data frame [59,140 x 3]
diversity position GC.binned
(dbl) (dbl) (fctr)
1 0.0000000 55500.5 (51.6,68.5]
because the order of R commands was as follows:
setwd("~/bds-files/chapter-08-r")
d <- read.csv("Dataset_S1.txt")
colnames(d)[12] <- "percent.GC"
d$cent <- d$start >= 25800000 & d$end <= 29700000
d$diversity <- d$Pi / (10*1000) # rescale, removing 10x and making per bp
d$position <- (d$end + d$start) / 2
d$GC.binned <- cut(d$percent.GC, 5)
(Page 246)
d_df %>% filter(percent.GC > 40) becomes filter(d_df, percent.GC > 40.
should be
d_df %>% filter(percent.GC > 40) becomes filter(d_df, percent.GC > 40).
(Page 249) The Double Backslash
To actually include a black‐ slash in a string,
should be
To actually include a back‐ slash in a string,
(Page 249)
Unlike grep(), regexpr(pattern, x)
should be
Unlike grep(), regexpr(pattern, text)
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> sub(" *[chrom]+(\\d+|X|Y|M) *", "chr\\1", c("chr19", "chrY"), perl=TRUE)
was changed to
> sub(" *[chrom]+(\\d+|X|Y|M) *", "chr\\1", c("chr19", "chromY"), perl=TRUE)
in Japanese edition.
https://www.oreilly.co.jp/books/9784873118635/
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• RStudio’s Rmarkdown tutorial
http://bit.ly/rstudio-rmkdwn
The page doesn't exist. the page may have moved
https://rmarkdown.rstudio.com/
(Page 256)
https://stat.ethz.ch/R-manual/R-devel/library/base/html/args.html
Because there is the function args(), variable name of args should be avoided.
## args.R -- a simple script to show command line args
args <- commandArgs(TRUE) print(args)
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$ ls -l hotspots
[vinceb]% ls -l hotspots
should be
$ ls -l hotspots
(Page 261)
save.history()
should be
savehistory()
I got the following messages:
> savehistory()
Error in .External2(C_savehistory, file) :
'savehistory' is not currently implemented