s ComBat.mc function is from an R
package "Enmix". When typing library(Enmix), no error message, so the Enmix
library is installed. Can you tell me why I got this e
Hi Jim,
Thank you for the message! Yes, you are right, I contacted Dr. Xu Zongli, he
said he removed the ComBat.mc function from the new version.
Ding
From: Jim Lemon [mailto:drjimle...@gmail.com]
Sent: Wednesday, November 11, 2020 5:36 PM
To: Yuan Chun Ding
Cc: r-help@r-project.org
Subject
Dear R user,
I want to reshape a long data frame to wide format, I made the following
example files. Can you help me?
Thank you,
Yuan Chun Ding
sample <-c("xr" , "xr" , "fh" , "fh" , "fh" , "uy" , "uy" , "uy"
t; warnings()
Warning messages:
1: In reshapeWide(data, idvar = idvar, timevar = timevar, ... :
multiple rows match for Tumor_Sample_Barcode=TCGA-A8-A09Z-01A-11W-A019-09:
first taken
2: In reshapeWide(data, idvar = idvar, timevar = timevar, ... :
From: Bert Gunter [mailto:bgunter.4...@gmail.
Hi Rui,
Thank you so much!! You code works well and I am looking into the pivot_wider
function.
Yuan Ding
-Original Message-
From: Rui Barradas [mailto:ruipbarra...@sapo.pt]
Sent: Thursday, January 7, 2021 12:19 PM
To: Yuan Chun Ding ; r-help@r-project.org
Subject: Re: [R] non
dom numbers across different
zero values. If all zero values in one row are replaced by the same 1.13,
then sd in that row is zero, causing other problem in the following calculation.
Can you help me?
Thank you,
Yuan chun D
Hi Bert and Rui,
Thank you very much! I had thought for every condition of matrix ==0 ,
rnrom(n=1, 1, 0.1) will randomly generate a number with mean 1 and sd 0.1.
Yuan
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Friday, January 8, 2021 2:49 PM
To: Yuan Chun Ding
Cc: r-help@r
Dear R user,
The following qqunit.plot function generated correct qq plot, however, I want
to make axis label (1 ,2 ,.8) have larger size for publication. I tried to
add cex.axis =1.2 code following the pch =20, but it does not change size of
axis label. I guess lattice library setting is
Dear R users,
I have a numeric table with 140 rows and 30 columns, here I only made partial
table, test1, as an example. I want to apply a blue color range to the value
in each cell of the data frame test1.
I found some R code using DT library. However, I only can see the colored table
at m
HSV or HCL). You may be interested in some of the plotting
functions in plotrix that employ color.scale, particularly "size_n_color".
Jim
On Fri, Jun 18, 2021 at 10:04 AM Yuan Chun Ding wrote:
>
> Dear R users,
>
> I have a numeric table with 140 rows and 30 columns, here I only ma
Hi R users,
In this test file,
test <- data.frame(group1=c("g1", "g1", "g1", "g2", "g2", "g2", "g2", "g2",
"g2"),
group2=c("k1", "a2", "a2", "c5", "n6",
"n6", "n6", "m10","m10"),
count= c( 1, 1,2, 1, 2,
summarise(Number_of_region =
n_distinct(group2))
Ding
-Original Message-
From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us]
Sent: Friday, July 2, 2021 3:36 PM
To: r-help@r-project.org; Yuan Chun Ding ; r-help@r-project.org
Subject: Re: [R] add a variable a data frame to sequentia
2,
1, 2, 2, 2,3,3 ));
I want to get count column.
the summary count is below.
count_test <- test %>% group_by(group1 ) %>%summarise(Number_of_region =
n_distinct(group2))
Thank you,
Ding
-Original Message-
From: Bert Gunter [mailto:bgunter.4...@gmail.c
1,2,
2, 2, 3,3 ));
I also thought about removing of duplicates first and then doing a merge. For
some reason, I thought one line of code from tidyverse library could do it .
Thank You,
Ding
-Original Message-
From: Jeff Newmiller [
years ago.
Ding
-Original Message-
From: Avi Gross [mailto:avigr...@verizon.net]
Sent: Friday, July 2, 2021 5:14 PM
To: Yuan Chun Ding ; r-help@r-project.org
Subject: RE: [R] add a variable a data frame to sequentially count unique rows
Ding,
Just to get you to stop asking, here is a soluti
Hi R users,
I have a folder (called genotype) with 652 files; the file names are
GTEX-1A3MV.out, GTEX-1A3MX.out, GTEX-1B8SF.out, etc; in each file, only one
column of data without a header as below
201
2/2
238
3/4
245
1/2
.
983255
3/3
983766
None
A total of 20528 rows;
I need to read al
erge all 652 files into one file with VNTRid as first column, 2nd to 653th
column are genotype with header
#as sample ID, so
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Thursday, December 19, 2019 6:52 PM
To: Yuan Chun Ding
Cc: r-help@r-project.org
Subject: Re: [R] data reshape
__
Hi Bert,
Thank you for the elegant code example. I achieved my goal using lapply
function and do.call function together. Reduce function is nicer one and I am
looking into it.
Ding
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Friday, December 20, 2019 11:47 AM
To: Yuan Chun Ding
Hi R users,
in a Shiny test code, choices = list(1, 2, 3), it generates three components
in the choice list, my code works fine and generated tables and plots I want.
now I want to modify to choices = list (1, 2, 3, , 5211). list (seq(1,
5211,1) does not work, it generates one component
Hi Rolf,
Yes,
choices = as.list(seq(1,5211,1))
is what I want.
Thank you so much,
Ding
From: Rolf Turner [r.tur...@auckland.ac.nz]
Sent: Wednesday, January 1, 2020 3:29 PM
To: Yuan Chun Ding; r-help@r-project.org
Subject: Re: [R] a simple question
Hi R users,
Does any one know a R package for genetic analysis of VNTR (variable number of
tandem repeats) genotype data? For example, performing Hardy Weinberg
equilibrium test, calculating heterozygosity and polymorphism information
content etc.
I am sorry if this question is not relevant to t
When you do x1g$fdr, you adjusted for a total of 15568 tests, so FDR is high
for those first four entries. When you do p.adjust(pval,method="BH"), you
assumed there were only a total of 4 multiple tests in your experiment, so FDR
is low.
Ding
-Original Message-
From: R-help [mailto:r
Hi R users,
We like to use shiny program to share data view between collaborators in
different universities.
When running shiny, I got the following errors, so I just found that I am
allowed to upload up to five applications. I want to remove the first four old
applications (not view those pl
Thank you for pointing me there.
Ding
-Original Message-
From: peter dalgaard [mailto:pda...@gmail.com]
Sent: Thursday, March 05, 2020 2:21 PM
To: Yuan Chun Ding
Cc: r-help@r-project.org
Subject: Re: [R] how to archive old shiny applications
That'll be between you and the peopl
Hi R users,
I want to find multiple modes (10, 8, 149) for the following vector.
freq =1,2,5,5 10,4,4,8,1,1,8,8,2,4,3,1,2,1,1 138 149 14,1,1;
any suggestion?
Thank you,
Ding
--
--
tem4 <-as.data.frame(t(t(table(tem3$VNTR_repeats[,c(1,3)]
tem4$Var1 <-as.numeric(as.character(tem4$Var1))
tem4 <-tem4[order(tem4$Var1),]
m<-
____
From: Abby Spurdle [spurdl...@gmail.com]
Sent: Sunday, March 15, 2020 3:42 PM
To: Jim Lemo
rettyR)
>>> Mode(freq)
>> [1] "1"
>>
>> You have a single modal value (1). If there were at most two ones, you
>> would have three values (2,4,8) that could be considered multiple
>> modes. What you seem to be doing is considering values that are not
&g
nal packages. I admit that what I am doing is
pretty explorative.
On Sun, Mar 15, 2020 at 9:11 PM Yuan Chun Ding
mailto:ycd...@coh.org>> wrote:
sorry, I just came back.
Yes, Abby's understanding is right.
> tem4$Var1
[1] 13 4 5 67 8 9 10 11 12 13 14 15
-Original Message-
From: Jim Lemon [mailto:drjimle...@gmail.com]
Sent: Monday, March 16, 2020 1:10 AM
To: Yuan Chun Ding; r-help mailing list
Subject: Re: [R] find multiple mode, sorry for not providing enough information
[Attention: This email came from an external source. Do not open
ints=TRUE),]
-Original Message-
From: Abby Spurdle [mailto:spurdl...@gmail.com]
Sent: Monday, March 16, 2020 1:57 PM
To: Yuan Chun Ding
Cc: Jim Lemon; r-help mailing list
Subject: Re: [R] find multiple mode, sorry for not providing enough information
(Sorry, that was supposed to go to the
Hi R users,
I generated 2972 list files in R, each list includes four data frame files ,
file names for those list file are VNTR13576, VNTR14689, etc. the second data
frame in each list has the same 11 column names, but different number of rows.
I can combine two dataframes by
list2972 <-ls(pa
Hi Bert,
Yes, your code works very well.
Thank you very much!!
Ding
From: Bert Gunter [bgunter.4...@gmail.com]
Sent: Wednesday, March 18, 2020 1:02 PM
To: Yuan Chun Ding
Cc: r-help mailing list
Subject: Re: [R] row combining 2972 files
Untested in the absence
ned <- data.table::rbindlist(keep)
HTH,
Denes
>
> should do it.
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comi
Hi R users,
I want to do a data reshape from long to wide, I thought it was easy using
tidyverse spread function, but it did not work well. Can you help me?
Thank you,
Ding
test1 data frame is long file and test2 is the wide file I want to get
test1 <- data.frame (vntr1=c("v1","v1", "v2","v2"
Rui Barradas [ruipbarra...@sapo.pt]
Sent: Friday, April 3, 2020 12:08 PM
To: Yuan Chun Ding; r-help mailing list
Subject: Re: [R] a simple reshape
Hello,
It's a bit more complicated than you have coded it.
I will use pivot_wider, it's now the natural way of doing it.
test1 %>
: Yuan Chun Ding
Cc: r-help mailing list
Subject: Re: [R] a simple reshape
Hi,
[For a non-tidyverse solution:]
Your problem is ambiguous without a 'time' variable; e.g., why should
the answer not be
test2 <- data.frame(vntr1=c("v1","v2"),
Hi R users,
I want to create a new variable, Ravg, in data frame tem2 based on values of
two other variables m1 and m2.
the condition:
if m1 = 23 and m2 =23 then Ravg =23;
else if m1 != 23 and m2=23 then Ravg =m1;
else if m1 =23 and m2 !=23 then Ravg=m2;
else Ravg=average of m1 and m2;
the R
confused when there are more
than two conditions inside of ifelse function. I will look into ifelse function
Thank you,
Ding
From: Thierry Onkelinx [thierry.onkel...@inbo.be]
Sent: Tuesday, April 7, 2020 11:48 AM
To: Yuan Chun Ding
Cc: r-help mailing list
Subject: Re: [R] to create a new
Hi Bert,
your code worked perfect. you always make me learn new R code skills!
Thank you so much!!
Ding
From: Bert Gunter [bgunter.4...@gmail.com]
Sent: Tuesday, April 7, 2020 12:53 PM
To: Yuan Chun Ding
Cc: r-help mailing list
Subject: Re: [R] to
Hi R Users,
I tried to use sql in R; test1 works well,
library(sqldf)
test1 <- sqldf("select * from r where V1 like
'%GCCATGTCAGCACACTACC%TGAAACCTTTAACTATTT%'")
test2 <- sqldf("select * from r where V1 like markerinfo$flank1[1] ")
but I want to store the search content in a markerinfo file as
Thank you, Sarah, I modified your suggestion a little and it works.
Ding
-Original Message-
From: Sarah Goslee [mailto:sarah.gos...@gmail.com]
Sent: Sunday, June 28, 2020 2:01 PM
To: Yuan Chun Ding
Cc: r-help@r-project.org
Subject: Re: [R] help with sqldf
[Attention: This email came
Dear R users,
I generated a boxplots in combination of dotplots using the R code below for
the attached test file.
boxplot(value~score, data = test, outpch = NA, xlab="",ylab="",xaxt='n',
cex.lab=1.2, cex.axis=1.2, main="Correlation of SCNV score and SCNV
value ")
mtext(side=2, "SCNV val
Hi R users,
I thought the follow R code should work, but I got error, Can you fix my code?
Thank you,
Ding
outlier_tcga_MAD3 <- outlier_tcga %>% filter(n_two >0) %>%
mutate(freqMAD3_gain2ratio = N_MAD3_gain2/n_two )%>%
if (N_MAD3 < 9) {filter(freqMAD3_gain >=1)} else if (N_MAD3 > n_t
it only generated one column of summary.
Do you know why?
Thank you,
Yuan Chun Ding
summary_anno1148ft <- anno1148ft %>%
pivot_longer(c(t_depth, t_alt_count, t_alt_ratio), names_to = "measure") %>%
group_by(dat, measure) %>%
summarize(minimum = min(value,na.rm=T),
down.
Thank you,
Ding
From: CALUM POLWART
Sent: Wednesday, June 12, 2024 10:52 AM
To: Yuan Chun Ding
Cc: r-help@r-project.org
Subject: Re: [R] my R code worked well when running the first 1000 lines of R
code
I sometimes think people on this list are quite rude to posters. I'm afrai
: Rui Barradas
Sent: Wednesday, June 12, 2024 11:29 AM
To: Yuan Chun Ding ; CALUM POLWART
Cc: r-help@r-project.org
Subject: Re: [R] my R code worked well when running the first 1000 lines of R
code
Hello, Inline. Às 19: 03 de 12/06/2024, Yuan Chun Ding via R-help escreveu: > I
am sorry that I know
Hi R users,
I generated a square correlation matrix for the dat dataframe below;
dat<-data.frame(g1=c(1,0,0,1,1,1,0,0,0),
g2=c(0,1,0,1,0,1,1,0,0),
g3=c(1,1,0,0,0,1,0,0,0),
g4=c(0,1,0,1,1,1,1,1,0))
library("Hmisc")
dat.rcorr = rcorr(as.matrix(dat))
da
HI Rui,
Thank you for the help!
You did not remove a row if zero values exist in both column pair, right?
Ding
From: Rui Barradas
Sent: Thursday, July 25, 2024 11:15 AM
To: Yuan Chun Ding ; r-help@r-project.org
Subject: Re: [R] please help generate a square correlation matrix
Às 17: 39 de
.test(tem2[,1],tem2[,2])
r[i, j] <- tmp3$estimate
P[i, j] <- tmp3$p.value
}
}
}
r<-as.data.frame(r)
P<-as.data.frame(P)
From: R-help On Behalf Of Yuan Chun Ding via
R-help
Sent: Thursday, July 25, 2024 11:26 AM
To: Rui Barradas ; r-help@r-project.org
Subject: Re: [
, i], dat[k, j]) : the standard deviation is zero
> >
> > The NA and warning comes in the 2,4 pair of columns because after
> > removing all zero rows in the pair, dat[,4] is all 1's, giving a zero
> > in the denominator of the cor() calculation -- again, assum
my case, we measured all mutations for all 1000 samples using an exactly
same sequencing method, so no issue of never-reporting.
I am very grateful for help and comments from Rui, Richard and Bert!!
Ding
From: Bert Gunter
Sent: Saturday, July 27, 2024 4:50 PM
To: Yuan Chun Ding
Cc: Richard
Dear R users,
I am running the following code below, the gem751be.rpkm is a dataframe with
dim of 751 samples by 35164 variables, 73 phenotypic variables in the furst to
73rd column and 35091 genomic variables or genes in the 74th to 35164th
columns. What I need to do is to calculate the res
0.99.
I have not found the reason.
Thanks,
Ding
From: Bert Gunter
Sent: Friday, August 9, 2024 7:11 PM
To: Ben Bolker
Cc: Yuan Chun Ding ; r-help@r-project.org
Subject: Re: [R] a fast way to do my job
Better idea, Ben! It would work as you might expect it to to produce the same
results as the
after add intercept, all residuals are the same from lm or lm.fit.
Ding
From: Bert Gunter
Sent: Saturday, August 10, 2024 1:00 PM
To: Yuan Chun Ding
Cc: Ben Bolker ; r-help@r-project.org
Subject: Re: [R] a fast way to do my job
Probably because you inadvertently ran different models. Without
You are right. I also just thought about that, no intercept is not applicable
to my case.
Ding
From: Bert Gunter
Sent: Saturday, August 10, 2024 1:06 PM
To: Yuan Chun Ding
Cc: Ben Bolker ; r-help@r-project.org
Subject: Re: [R] a fast way to do my job
Ah, messages crossed. A no-intercept
e.rpkm$purity2)
then running result2 <- residuals(lm.fit( x= pur2.1, y = dat));
now I am thinking whether an intercept is required or not.
Ding
From: R-help On Behalf Of Yuan Chun Ding via
R-help
Sent: Saturday, August 10, 2024 12:30 PM
To: Bert Gunter ; Ben Bolker
Cc: r-help@r-project.org
Subjec
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