[R] reviewer comment

-- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr # tel : 01 49 81 32 79 # Sec : 01 49 81 32 90

Re: [R] reviewer comment

be greatly appreciated! Regards ML -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie # H?pital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr

Re: [R] p-values from lm()

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly

[R] Draw vertical line segments between pairs of points

Dear all, How to add /*vertical*/ lines above bar graph to display p-values ( between pairs of points )? Regards ML -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly

[R] Multicollinearty in logistic regression models

Dear All, Is there a method to diagnostic multicollinearty in logistic regression models like vif indicator in linear regression ( variance inflation Factor ...) ? Thank you in advance M -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie

Re: [R] R packages for pathway analysis?

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H

Re: [R] Help to get fitted and residual value

. -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr # tel : 01 49 81 32 79 # Sec : 01

Re: [R] Combining histograms and distribution curve

, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr

Re: [R] quick ANOVA question

://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly

Re: [R] how to get AIC BIC information using funtion lm

. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed

Re: [R] changing date format in a dataframe

-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# P?le de Psychiatrie# H?pital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr # tel

Re: [R] determine frequencies in a matrix by row

. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE

Re: [R] write gene_id in a bed file

. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr# tel : 01 49 81 32 79 # Sec : 01 49 81 32 90

[R] Several Regression by combinations variables

Regards M -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr # tel : 01 49 81 32 79

[R] transpose ?

D as follow ( just for the first line) C (V7) C (V9) T G A C G C C (V8) C (V10) T G A C G C Any help would be appreciated Regards M -- Mohamed Lajnef,IE INSERM U955

[R] Fwd: transpose ?

Dear All, Sorry for the previous mail,suppose this data.frame D V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 V19 V20 V21 V22 C C C C T T G G A A C C G G C C G G T T A A A A T A T T C C G G C C C C T T G G A A C C G G

Re: [R] quantile function - I need only the quantile value itself

do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40

Re: [R] adding linear regression data to plot

-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de

Re: [R] create data set from selection of rows

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER

Re: [R] Plot confidence intervals

]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955

Re: [R] nrow()

Hi Sandra, What about ?is.na function ? Hope this help Regards, ML Le 22/02/11 16:11, Sandra Stankowski a écrit : NROW(data[jan,16] != NaN) -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER

Re: [R] sampling

-- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj...@inserm.fr # tel : 01 49 81 31 31 (poste 18467) # Sec : 01 49 81 32 90 # fax

Re: [R] removing lower and upper quantiles from an arry

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE

Re: [R] removing lower and upper quantiles from an arry

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE

Re: [R] darcs patch: Apply on data frame

: Scrip:ranksum- function(a){ g1- c(1, 2, 3) g2- c(4, 5, 6, 7, 8, 9, 10, 11, 12) c- wilcox.test(a[g1], a[g2]) return c$p.value } -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER

Re: [R] barplot with errorbars

and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE

Re: [R] Filter data

Hi Diogenas, Try this, data-subset(poli, poli$year1994) Best, M Diogenas dioge...@gmail.com a écrit : Hello, I understand that question is probably stupid, but ... I have data (polity IV index) country,year,democ,autoc,polity,polity2 1,Afghanistan ,1800,1,7,-6,-6 2,Afghanistan

[R] Path analysis with logistic regression

to do this? Any help would be appreciated Regards -- Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie# Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # mohamed.laj

Re: [R] which function

Hi Arnaud Try this l[((which(100420==l))-1):which(100420==l)] Regards Mo arnaud Gaboury arnaud.gabo...@gmail.com a écrit : Dear group, Here is a list of elements : l - c(100415, 100416, 100419, 100420, 100421, 100422, 100423, 100426, 100427, 100428, 100429, 100430, 100503, 100504,

Re: [R] R eat my data

...@nuuk:~/operon$ wc -l id_name_gh5.txt 1932 id_name_gh5.txt gene_name-read.table(/home/cdu/operon/id_name_gh5.txt, sep=\t, skip=0, header=F, fill=T) dim(gene_name) [1] 10683 -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue

Re: [R] R eat my data

cheks the comments sent by David! M Changbin Du a écrit : length(count.fields(/home/cdu/operon/id_name_gh5.txt)) [1] 1932 It is 1932 lines when count in R On Tue, May 25, 2010 at 8:52 AM, Mohamed Lajnef mohamed.laj...@inserm.fr mailto:mohamed.laj...@inserm.fr wrote: Hi Changbin

Re: [R] sort a data.frame

The solution given by Jim is more correct dd[order(as.numeric(substr(dd$b,4,5))),] regards M jim holtman a écrit : dd b x y z 1 chr2 A 8 1 2 chr1 D 3 1 3 chr15 A 9 1 4 chr13 C 9 2 # add column with just numbers dd$sort - as.integer(gsub(\\D+, , dd$b)) dd[order(dd$sort),] #

[R] t.test per line

~ group1,m) } ttest- apply(data, 1, fun) Error in t.test.default(x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, : data are essentially constant Any help would be appreciated ML Best -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly 94010

Re: [R] timing a function

Hi, ? proc.time() for more help regards Ml pdb ph...@philbrierley.com a écrit : Hi, I want to time how long a function takes to execute. Any clues on what to search for to achieve this? Thanks in advance. -- View this message in context:

Re: [R] Find solution for an error in the condition of if

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly 94010 CRETEIL Cedex FRANCE mohamed.laj...@inserm.fr tel : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49

Re: [R] apply fun to df returning a matrix

mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly

Re: [R] median Q?

commented, minimal, self-contained, reproducible code. -- Joshua Wiley Senior in Psychology University of California, Riverside http://www.joshuawiley.com/ -- ** Vlatka Matkovic Puljic 095/8618 171 -- Mohamed Lajnef,IE INSERM U955 eq 15

Re: [R] sum specific rows in a data frame

-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly 94010 CRETEIL Cedex FRANCE mohamed.laj...@inserm.fr tel : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81 30 99

Re: [R] compare multiple values with vector and return vector

Hi Joris Try Is.element function: is.element (x,y) Regards mohamed Joris Meys jorism...@gmail.com a écrit : Dear all, I have a vector, and for each element I want to check whether it is equal to any element from another vector. I want a vector of logical values with the length of the first

Re: [R] Is the aggregate function the best way to do this?

-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital

Re: [R] Is the aggregate function the best way to do this?

Hi Bert, apply(data,1,max) gives the max value for each row in the data M Bert Jacobs a écrit : Hi Mohamed, Thx for the answer. And what should I do if my fun function is not 'sum' but 'max'? Bert -Original Message- From: Mohamed Lajnef [mailto:mohamed.laj...@inserm.fr] Sent: 17

[R] Empirical Pvalue

Dear R users, Can someone explain me the interpretation of empirical p-value ( max(t)) used to test the genetic association with PLINK? Any help will be appreciated Regards M -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly 94010 CRETEIL

Re: [R] Error of Stepwise Regression with number of rows in use has changed: remove missing values?

do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly 94010 CRETEIL Cedex FRANCE mohamed.laj...@inserm.fr tel : 01

Re: [R] binary

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. Courriel : mohamed.laj...@inserm.fr tel.: 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81

Re: [R] Error in lm() function

(formula = dat[, 1] ~ dat[, -1], drop.unused.levels = TRUE) : invalid type (list) for variable 'dat[, -1]' Can anyone please tell me what to do? Best, -- Mohamed Lajnef INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. Courriel : mohamed.laj...@inserm.fr tel.: 01 49 81 31 31 (poste 18470

Re: [R] how to suppress the output from stepAIC?

Hi Jack, try stepAIC with trace parameter: stepAIC(...,trace=FALSE) Regards, M Jack Luo jluo.rh...@gmail.com a écrit : Hi, I am now running a cross-validation using coxph coupled with stepAIC for model selection, is there anyway to suppress the output? It's too much. -Jack

Re: [R] How to sum and group data by DATE in data frame

, self-contained, reproducible code. -- Mohamed Lajnef INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. Courriel : mohamed.laj...@inserm.fr tel. : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81 30 99 __ R-help@r-project.org

Re: [R] Averaging rows if a condition is true.

/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. Courriel : mohamed.laj...@inserm.fr tel. : 01 49 81 31 31

Re: [R] Select top three values from data frame

-contained, reproducible code. -- Mohamed Lajnef INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. Courriel : mohamed.laj...@inserm.fr tel. : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81 30 99 __ R-help@r-project.org mailing list

Re: [R] Select top three values from data frame

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef INSERM Unité 955. 40 rue de Mesly. 94000 Créteil. Courriel : mohamed.laj...@inserm.fr tel. : 01 49 81 31 31 (poste 18470) Sec : 01 49

Re: [R] Package read large file

Dear Jim Michael the file contains 1000 lines and 1.200.000 columns, txt format and i wish to read all the file with R if possible, or read a few columns? I tried without success to turn bigmemory and colbycol packages, also scan and readLines function but It takes a long time without

[R] Package read large file

Dear R-Users, I am looking for packages that could read large files in R? any suggestions are welcome. Regards, ML __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide