Hello,
I have 3 groups,let's call them g1, g2, g3. Each of them is a result
of analysis in between groups of conditions, and g1 looks like this
geneSymbol logFC t P.Value
adj.P.Val Beta
EXykpF1BRREdXnv9Xk MKI67 -0.3115880 -5.521186
Can you please get back to me about this, I need this meta p values
for manuscript I have to submit next week
On Wed, Oct 30, 2019 at 5:35 PM Ana Marija wrote:
>
> I also tried to do it this way:
>
> d$META <- sapply(seq_len(nrow(d)), function(rn) {
> unlist(sumz(as.matr
wr
"numeric"
> sum(is.na(d$LCL))
[1] 0
> sum(is.na(d$Retina))
[1] 0
> sum(is.na(d$wl))
[1] 0
> sum(is.na(d$wr))
[1] 0
> dim(d)
[1] 1668837 7
On Wed, Oct 30, 2019 at 4:52 PM Ana Marija wrote:
>
> Hi Michael,
>
> this still doesn't work, by data fra
rry about that, I
> should have thought of it before.
>
> When I next update metap I will try to get it to degrade more gracefully
> when it finds an error.
>
> Michael
>
> On 28/10/2019 19:06, Ana Marija wrote:
> > Hi Michael,
> >
> > I tried what you pr
415e-01,
>> 2.459322e-02,2.873351e-01,8.477168e-01,1.351068e-02,
>> 1.053550e-01,4.812686e-01,1.404957e-01,9.835912e-02,4.373995e-01,
>> 8.803856e-02)
>> qval_obj=qvalue(pvals)
>> qval_obj$pi0
>> [1] 0.1981095
>> pi1=1-qval_obj$pi0
>> pi1
>&g
hr) & (l4join$X2 %in% ajoin$pos)
> i2 <- (ajoin$chr %in% l4join$X1) & (ajoin$pos %in% l4join$X2)
>
> rm(l4join, ajoin) # don't need this any more, remove them
>
> # now the real fread's
> l4 <- data.table::fread(l4_file)
> asign <- data.table::fread(asign_file)
>
fer not to install packages in my
> script but just to use `library` and manually get each of the packages that
> `library` complains about onto my machine. Once done, the script runs just
> fine after that.
>
> On October 28, 2019 4:08:03 PM PDT, Ana Marija
> wrote:
>
f) :
missing or infinite values in inputs are not allowed
On Mon, Oct 28, 2019 at 6:02 PM Ana Marija wrote:
>
> can you please send me command you used to install it?
>
> On Mon, Oct 28, 2019 at 5:12 PM Jim Lemon wrote:
> >
> > Hi Ana,
> > Seems to work without er
1.053550e-01,4.812686e-01,1.404957e-01,9.835912e-02,4.373995e-01,
> 8.803856e-02)
> qval_obj=qvalue(pvals)
> qval_obj$pi0
> [1] 0.1981095
> pi1=1-qval_obj$pi0
> pi1
> [1] 0.8018905
>
> Jiim
>
> On Tue, Oct 29, 2019 at 8:45 AM Ana Marija
> wrote:
&g
Hello,
I am trying to calculate True Positive Rate, TPR with this procedure:
pvals=q$METAge
qval_obj=qvalue(pvals) #is false discovery rate
pi1=1-qval_obj$pi0 #TPR
pi1 #TPR
But I am getting this error:
Error in smooth.spline(lambda, pi0, df = smooth.df) :
missing or
gt; There must be several ways of doing this but see below for an idea with
> comments in-line.
>
> On 26/10/2019 00:31, Ana Marija wrote:
> > Hello,
> >
> > I would like to use this package metap
> > to calculate multiple o values
> >
> > I have
this is the function I was referring to:
https://www.rdocumentation.org/packages/metap/versions/1.1/topics/sumz
On Fri, Oct 25, 2019 at 6:31 PM Ana Marija wrote:
>
> Hello,
>
> I would like to use this package metap
> to calculate multiple o values
>
> I have my data
Hello,
I would like to use this package metap
to calculate multiple o values
I have my data frame with 3 p values
> head(tt)
RSG E B
1: rs2089177 0.9986 0.7153 0.604716
2: rs4360974 0.9738 0.7838 0.430228
3: rs6502526 0.9744 0.7839
I am using R-3.6.1
and these libraries:
library(data.table)
library(dplyr)
On Wed, Oct 23, 2019 at 6:54 PM Duncan Murdoch wrote:
>
> On 23/10/2019 7:04 p.m., Ana Marija wrote:
> > I also tried left_join but I got: Error: std::bad_alloc
> >
> >> df3 <- left_joi
no can you please send me an example how the command would look like in my case?
On Wed, Oct 23, 2019 at 6:16 PM Jim Lemon wrote:
>
> Yes. Have you tried the bigmemory package?
>
> Jim
>
> On Thu, Oct 24, 2019 at 10:08 AM Ana Marija
> wrote:
> >
> > Hi Jim,
tly the best way to do it if you
> have a database manager is to read the two datasets into tables and do
> the join via SQL or whatever language is available.
>
> Jim
>
> On Thu, Oct 24, 2019 at 10:17 AM Ana Marija
> wrote:
> >
> > no can you please send me an
X2 X3 X4 X5
> [6] variant_id pval_nominal gene_id.LCL gene chr_pos
> [11] p.val.Retina
> <0 rows> (or 0-length row.names)
>
> It works okay, but there are no matches in the join. So I can't even
> guess what the problem is.
I also tried left_join but I got: Error: std::bad_alloc
> df3 <- left_join(l4, asign, by = c("chr","pos"))
Error: std::bad_alloc
> dim(l4)
[1] 166941635 8
> dim(asign)
[1] 107371528 5
On Wed, Oct 23, 2019 at 5:32 PM Ana Marija wrote:
>
>
Hello,
I have two data frames like this:
> head(l4)
X1X2 X3 X4 X5 variant_id pval_nominal gene_id.LCL
1 chr1 13550 G A b38 1:13550:G:A 0.375614 ENSG0227232
2 chr1 14671 G C b38 1:14671:G:C 0.474708 ENSG0227232
3 chr1 14677 G A b38 1:14677:G:A 0.699887
er
>
> "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" comic strip )
>
>
> On Tue, Oct 22, 2019 at 6:18 PM Ana Marija
> wrote:
>>
>
Hello,
I would like to calculate a p value from two distributions, one looks like this:
> head(b)
gene_id number_of_eqtles_per_gene
1: ENSG0237683.5 5
2: ENSG0225972.1 267
3: ENSG0225630.197
4:
tot$newcol <- -9
> tot$newcol[e10] <- 1
> tot$newcol[e11] <- 2
>
>
> On both cases the 2 lines sapply/rowSums can be made one with
>
> rowSums(sapply(...)) > 0
>
>
> Hope this helps,
>
> Rui Barradas
>
> Às 20:52 de 05/10/19, Ana Marija escreveu:
>
Hello,
I have a data frame tot which has many columns and many rows.
I am trying to find all columns that have say a value in any of their
rows that STARTS WITH: "E94"
for example there are columns like this:
> unique(tot$diagnoses_icd9_f41271_0_44)
[1] NA "E9420"
I tried:
Hello,
I have a dataframe (t1) with many columns, but the one I care about it this:
> unique(t1$sex_chromosome_aneuploidy_f22019_0_0)
[1] NA"Yes"
it has these two values.
I would like to remove from my dataframe t1 all rows which have "Yes"
in t1$sex_chromosome_aneuploidy_f22019_0_0
I
een
> 70.42-7.75 or fold change 70.42/7.75. If they are absolute value you can
> also scale them in log scale and do the same. Hope this helps. Good luck.
>
> Vivek
>
> On Fri, Sep 27, 2019 at 9:32 PM Ana Marija
> wrote:
>
>> Hi Vivek,
>>
>> Thanks for getting back
Hi,
I created a bar plot with this code:
library(ggplot2)
df <- data.frame("prop" = c(7.75,70.42), "Name" = c("All Genes","RG Genes"))
p<-ggplot(data=df, aes(x=Name, y=prop,fill=Name)) +
geom_bar(stat="identity")+ labs(x="", y = "Proportion of cis
EQTLs")+ scale_fill_brewer(palette="Greens") +
Hello,
I tried using qvalue function:
library(qvalue)
qval_obj=qvalue(pvalR)
pi1=1-qval_obj$pi0
but after running:
qval_obj=qvalue(pvalR)
Error in smooth.spline(lambda, pi0, df = smooth.df) :
missing or infinite values in inputs are not allowed
or
Hello,
I made plot in attach using:
boxplot(flcn_M~subject,data=dx,col =
c("royalblue1","palevioletred1"),xlab="subjects",ylab="Expression
estimate in delta (log2)",boxwex = 0.2,frame.plot = FALSE)
stripchart(flcn_M~subject, vertical = TRUE, data = dx,method =
"jitter", add = TRUE,pch = 20,
does this look ok:
pt$pheno=ifelse(pt$phenoQ==-9 & pt$phenoH==-9,-9,ifelse(pt$phenoH==2 |
pt$phenoQ==2,2,1))
On Wed, Aug 7, 2019 at 1:40 PM Ana Marija wrote:
>
> Hello,
>
> I have a data frame which looks like this:
>
> > head(pt)
> eidQ phenoQ phenoH
> 1 10
Hello,
I have a data frame which looks like this:
> head(pt)
eidQ phenoQ phenoH
1 117 -9 -9
2 125 -9 -9
3 138 -9 1
4 142 -9 -9
5 156 -9 -9
6 174 -9 -9
7 138 -9 1
8 1000127 2 1
9 1000690
tor of 1s to controls before joining the datasets.
>
> On Tue, Aug 6, 2019 at 3:01 PM Ana Marija
> wrote:
> >
> > I really don't know how I would implement this
> >
> > On Tue, Aug 6, 2019 at 1:42 PM Patrick (Malone Quantitative) <
> mal...@malonequantitat
e.
>
>
> On Tue, Aug 6, 2019 at 2:38 PM Ana Marija
> wrote:
> >
> > Hi Patrick,
> >
> > yes both controls and tot have "eid" column, please see attached
> >
> > Can you please tell em what means to post in "plain text" ?
> &g
have some kind of ID variable? If so, it should be
> straightforward with the appropriate joining function.
>
> What have you tried?
>
> Also, please post in plain text.
>
>
> On Tue, Aug 6, 2019 at 2:16 PM Ana Marija
> wrote:
> >
> > Hello,
> >
> > I am
Hello,
I am filtering my data frame "tot" via:
controls=tot %>% filter_all(any_vars(. %in% c("E109", "E119","E149"))) %>%
filter_all(any_vars(. %in% c("Caucasian"))) %>% filter_all(any_vars(. %in%
c("No kinship found","Ten or more third-degree relatives identified")))
> dim(controls)
[1] 15381
Thank you so much! Just to confirm here MARGIN=1 indicates that "A" should
appear at least once per row?
On Mon, Jul 29, 2019 at 1:53 PM Eric Berger wrote:
> df$case <- apply(df,MARGIN = 1,function(v) { as.integer("A" %in% v) })
>
>
> On Mon, Jul 29,
which would be named "case" and
values inside would be: 1,1,0,1,1,1,0,0,1,1
so "case" column is where value "A" can be found in any column.
On Mon, Jul 29, 2019 at 12:53 PM Eric Berger wrote:
> You may have a typo/misstatement in your question.
> You define a
I have data frame which looks like this:
df=data.frame(
eye_problemsdisorders_f6148_0_1=c(A,C,D,NA,D,A,C,NA,B,A),
eye_problemsdisorders_f6148_0_2=c(B,C,NA,A,C,B,NA,NA,A,D),
eye_problemsdisorders_f6148_0_3=c(C,A,D,D,B,A,NA,NA,A,B),
eye_problemsdisorders_f6148_0_4=c(D,D,NA,B,A,C,NA,C,A,B),
;
> > Sent from my iPhone
> >
> > > On Jul 10, 2019, at 1:09 PM, Patrick (Malone Quantitative) <
> mal...@malonequantitative.com> wrote:
> > >
> > > First response: The ID column in your data is labeled "eid" but your
> > > function call re
y to list.
>
> On Wed, Jul 10, 2019, 6:08 PM Ana Marija
> wrote:
>
> > Hi Patrick,
> >
> > thanks for getting back to me, I tried that:
> >
> > > ukb_icd_diagnosis(my_ukb_data, eid = "117", icd.version = 10)
> > Error in ukb_icd_diagnosi
Hello,
I am trying to use this program:
https://github.com/kenhanscombe/ukbtools
> my_ukb_data[1:3,1:3]
eid sex_f31_0_0 year_of_birth_f34_0_0
1 117 Female 1938
2 125 Female 1951
3 138Male 1961
>
Hello,
I am trying to run this program FUSION.assoc_test.R from :
http://gusevlab.org/projects/fusion/#typical-analysis-and-output
[t.cri.asokovic@cri16in002 fusion_twas-master]$ Rscript FUSION.assoc_test.R
\
> --sumstats /gpfs/data/stranger-lab/anamaria/meta_gwas/META_CHR22_1.txt \
> --weights
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