kaustubhad / fastman Goto Github PK

fastqq appears to expect parameter to be named p1 instead of p. Function worked once I looked at the code itself, but couldn't find that in the vignette downloaded with the package

Hi,
I tried this:

> p = runif(100, min=0, max=1)
> fastqq(p1=p)

Hi, is there an option to put a title on the plot? I need this because I have supplementary figures where there will be many plots and they need to be labeled.

Thanks!

Hi, I want to color all points above the threshold as one color. I thought I could set a hex code for col, i.e. col="#DC7633", but that doesn't work. Any help would be appreciated. Thanks!

I am running the following code:
install.packages("remotes", repos = "http://cran.us.r-project.org", lib="/z/Comp/lu_group/Members/jwlorge/ATN/R")
remotes::install_github("danioreo/fastman",lib = "/z/Comp/lu_group/Members/jwlorge/ATN/R")
Which gives me the following error:
Error: package or namespace load failed for ‘fastman’ in namespaceExport(ns, exports):
undefined exports: fastman
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/z/Comp/lu_group/Members/jwlorge/ATN/R/fastman’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpZYg1zb/file12c3d26c90b542/fastman_0.1.0.tar.gz’ had non-zero exit status

When searching online, I found someone who had the same issue for a different function and it looked like it had to be fixed by github itself? I would appreciate any help or advice!

Hello,

I would like to add labels to the significant SNPs, but the labels are overlapping. Is there any option to remove the overlapping labels? Any help would be appreciated. Thanks!

Hi,

I have a plot where the signals I got go to 10-3 only...
So the plot automatically sets the ylim to 4...
I am trying to set it to 10 because even though it is far from my signals I would like to draw a significant line at around 5...

When I try to set the maxP = 10 nothing happens.
When I try to set the maxP = 2 for example, it works...

Is there a way to set the ylim when it is above the signals you got?

Best,
Guilherme

First, thank you for developing this package. I have GWAS data with > 20 million markers and could not plot it with qqman.

I would like to add vertical lines to my Manhattan plot to indicate specific sites on the genome. This is possible in the qqman package, as discussed in stephenturner/qqman#23. However, when I use abline() after fastman(), no line is drawn on the plot.

How can I add vertical lines to a Manhattan plot in fastman?

Thank you.

Hi,
Thanks for the package!. Is there a way to define the length of each Chr so that two manhattan plots can be compared to each other with the same x-scale and length of each chromosome? Or the only way is to input missing values for all the sites without calls?

Thanks.

Hi,
I would like to annotate my top hits with gene names rather than SNP IDs. Is it possible within the fastman package if I already have the gene name column in my results?

Hi,
I am overlaying k-mers over snp-based association in Manhattan plot where if I don't change the size of highlighted k-mers associations , I can't differentiate them as the highlighted ones hide the other set. Is it possible with fastman?
Thanks,

Vinod

Hello,

I was wondering if you know why this error would come up. It seems to think the SNP column has zero-length but as you can see from the screenshot the SNP column is fine...

I used the same genotype dataset for multiple phenotypes that worked, but randomly this one refuses to work.

Your input is appreciated! Thanks.

fastman(file2,
snp="SNP",
chrlabs = as.character(1:22),
speedup = TRUE,
colAbovePval =TRUE,
annotateN=4,
annotatePval=-log10(1e-6),
annotationAngle = 60,
annotationWinMb=60,
suggestiveline = -log10(1e-5),
genomewideline = -log10(5e-8),
cex=0.8, cex.text=0.6, cex.axis=0.7,
col=c("#36E072"), sortchr=TRUE
)

Error in text.default(x = m2$BPn + fac/7, y = m2$logP + fac/7, labels = m2$SNP, :
zero-length 'labels' specified

Hi, one possible upgrade that would help a lot is calculating the annotationWinMb across chromosomes. For example, a SNP label at the end of one chromosome and the beginning of the next will often overlap. These labels are super small and fully upright and still we have some interference:

Thanks!

Hi,
Fastqq seems not working.

data = fread('data.qassoc')
fastqq(p1 = data[['P']])
Error in round(ms$p, digits = digs) :
non-numeric argument to mathematical function

• I use R v4.2

Hi,
What is the license for the fastman package?
Thanks!

I'm unable to install the package using devtools:

> devtools::install_github("kaustubhad/fastman")
Downloading GitHub repo kaustubhad/fastman@HEAD
Error: Failed to install 'fastman' from GitHub:
  Does not appear to be an R package (no DESCRIPTION)

Is there a different, preferred method of installation?

Thanks!

Hi, what is the citation for use in publication?

Sorry for my very basic question. Is it possible to run fastman in a sliding window way? Thanks