Re: [R] How to retrieve data from a matrix
Thank you very much, It works! -- View this message in context: http://r.789695.n4.nabble.com/How-to-retrieve-data-from-a-matrix-tp4649721p4650036.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] How to retrieve data from a matrix
I have a data set (data.txt) containing information on affection status (1=affected; 0=not affected) for some subjects identified by an ID. Then I have a sort of correlation matrix of the same subjects (matrix.txt). For each affected subject in the data set I have to retrieve the IDs of unaffected subjects from the matrix (if the condition “affected-unaffected correlation0.0165” is satisfied) and such IDs should be placed in new columns of the data set on the affected subject corresponding row. Does anybody can help me? data.txt http://r.789695.n4.nabble.com/file/n4649721/data.txt matrix.txt http://r.789695.n4.nabble.com/file/n4649721/matrix.txt -- View this message in context: http://r.789695.n4.nabble.com/How-to-retrieve-data-from-a-matrix-tp4649721.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Script for searching in a kinship matrix
Hi everybody! I suceeded in extracting the sub-matrix containing just the relevant subjects of this example data (indeed I could retrieve 190 of the 220 subjects of the data example, so that the relative kinship matrix is a 190X190). For the subjects non present in the kinship matrix case-control kinship coefficient is to be supposed as 0 (zero) - no relatedness. I attach this example kinship matrix. KinExample.txt http://r.789695.n4.nabble.com/file/n4649178/KinExample.txt -- View this message in context: http://r.789695.n4.nabble.com/Script-for-searching-in-a-kinship-matrix-tp4649089p4649178.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] Script for searching in a kinship matrix
Hi everybody! In a case-control study I have already sampled cases stratifying for sex (0,1) and age (62y, =62y). I need to sample a group of controls with the same characteristics (which I can easily do) plus one more: the level of relatedness. Therefore controls should be matched to cases for sex (2 strata), age(2 strata) and, relatedness (less than a certain level). In particular I need that controls are as least as possible related to cases, for example each control should have a kinship coefficient less than 0.0156 (i.e. 1/64 as for second cousins) with its matched case. In the attached example data set (Example.txt) there are the sampled cases (20 cases: 5 subjects for each strata) and 200 possible controls I have already sampled stratifying for age and sex (50 subjects per strata). What I do not know is how to solve the relatedness problem. I have already computed the kinship coefficients matrix of the extended pedigree to whom the cases and controls in the example data belong. I do not provide it now because is a 4762 rows per 4762 columns matrix, and I do not know how to extract the sub-matrix containing just the relevant 220 subjects of this example data. As an example, such a kinship matrix for 5 subjects (ID: 51, 59, 119, 156 and 178) is like: 51 59 119 156 178 51 0.500 0.000 0.000 0.000 0.000 59 0.000 0.500 0.250 0.000 0.250 119 0.000 0.250 0.500 0.000 0.250 156 0.000 0.000 0.000 0.500 0.000 178 0.000 0.250 0.250 0.000 0.500 In conclusion I think I need a script that looks down such kinship matrix searching for controls satisfying the relatedness condition and that adds to my data set (Example.txt) as many columns as the maximum number of controls satisfying the relatedness condition for their matched cases. In particular in correspondence of each case (rows for which disease=1) the new columns should return the ID of the match control satisfying the condition:case-control kinship 0.0156 ; otherwise a missing value (such as NA). Such new columns will contain a value (ID code) only for cases and a missing value for controls. Does anybody can help me? Ginger Example.txt http://r.789695.n4.nabble.com/file/n4649089/Example.txt -- View this message in context: http://r.789695.n4.nabble.com/Script-for-searching-in-a-kinship-matrix-tp4649089.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] parsing text files
Hello, I have a .txt file with many clinical exams reports (two examples of which are attached to the message). I have to create a data frame with as many rows as the number of clinical exams reports in the text file and 24 columns: the first (to be labelled as ID) with a number (representing an identification code) which is the number in the 13th line of the clinical report following the string Acc.ne n. the second (to be labelled as DATE) with a date (indicating date of blood sampling), which is the date, again in the 13th line, following the identification code the following 22 columns (to be labelled with the name of parameters at lines from 20 to 41, as GLICEMIA ... COLESTEROLO LDL) I did search in the mailing list and tried to begin something like: #read the text file reports - readLines(ClinicalReports.txt) #processing the file starting at each Acc.ne n. serologic - lapply(which(grepl(^Acc.ne n., reports)), function(.line ) but I'm a biostatistician whith almost no expertise in programming and I really need your hepl! Please!!! http://r.789695.n4.nabble.com/file/n4456355/ClinicalReports.txt ClinicalReports.txt -- View this message in context: http://r.789695.n4.nabble.com/parsing-text-files-tp4456355p4456355.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] parsing text files
Ooops, I forgot to specify that for each raw, containing records of the clinical reports , the values of the 22 parameter measurement have to be reported. For example, first raw, first 5 columns: ID DATE GLICEMIA AZOTEMIA CREATININEMIASODIEMIA ...... ... 185 05/12/2011115 33.6 0.99 136 ...... ... -- View this message in context: http://r.789695.n4.nabble.com/parsing-text-files-tp4456355p4456389.html Sent from the R help mailing list archive at Nabble.com. __ 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.
