Objective how to assign a col-name to an empty header inside a list
My data structure Code should be placed in three backticks as shown below
results1 <- lapply(contrasts, function(x) results(dds, contrast=x)) ## my code
## Sample output
results1
$M0_vs_M1
log2 fold change (MLE): FAB M0 vs M1
Wald test p-value: FAB M0 vs M1
DataFrame with 51380 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000223972 1.35719895705297 0.167510490419353 0.46667402535746 0.358945390824022 0.719635942258462 0.856597394003598
ENSG00000227232 76.8560719439685 -0.705608168485163 0.219196495449407 -3.21906683333824 0.00128608506388972 0.0158343815011299
ENSG00000278267 4.90974256671574 -1.16851163038749 0.436136368072954 -2.67923456039794 0.00737906827756855 0.0508245749793705
ENSG00000243485 0.295581734786796 0.16890551310833 0.980082656456368 0.172338028834254 0.86317178889973 NA
ENSG00000237613 0.0612332522952744 0.265097343084784 3.52887790189744 0.0751222769544518 0.940117423456592 NA
... ... ... ... ... ... ...
ENSG00000215506 0.531980504702335 -0.554637704219196 0.843139724240875 -0.657824187703369 0.510651110092843 NA
ENSG00000224240 0.0555883982498256 -0.0875512872565122 3.56201998641903 -0.0245791117372503 0.980390680685091 NA
ENSG00000227629 0.0765793340097447 0.297144162185063 2.90839061586321 0.102167900200321 0.918623406325407 NA
ENSG00000237917 14.1547350663573 -0.0621818678501326 0.505199963776219 -0.12308367440358 0.90204083891314 0.956184083343483
ENSG00000231514 0.164301605186092 -0.5684666000495 1.47572077171201 -0.385212847136394 0.700079725794659 NA
$M0_vs_M2
log2 fold change (MLE): FAB M0 vs M2
Wald test p-value: FAB M0 vs M2
DataFrame with 51380 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
ENSG00000223972 1.35719895705297 0.546991630317625 0.476229496776925 1.14858830462962 0.250725781858858 0.507965684166553
ENSG00000227232 76.8560719439685 -0.62569393681632 0.218440258775195 -2.86437097412637 0.00417838341460869 0.0415066059471346
ENSG00000278267 4.90974256671574 -0.0129648769610915 0.445103345323286 -0.0291277904273554 0.976762671641514 0.99028984958177
ENSG00000243485 0.295581734786796 -0.846240912635684 0.969758036480007 -0.872630987114414 0.382864244993462 NA
ENSG00000237613 0.0612332522952744 0.258612647154544 3.51482364475393 0.0735777021246965 0.941346414163943 NA
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
In the above output this is the format for all the elements in the list
DataFrame with 51380 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
My objective is to add a col name to the empty header the column which is before the baseMean
.
I would like to save the output to do this Im running this
for(i in 1:length(results1)){
results = as.data.frame(results1[[i]])
write.table(results,file=paste0(names(results1)[i],"_TCGA_stages.txt"),sep = "\t",quote = FALSE,row.names = TRUE)
}
I get output like this
baseMean log2FoldChange lfcSE stat pvalue padj UP_DOWN
ENSG00000237973 10550.545143 -1.626252 0.3987092 -4.078792 4.527033e-05 0.0015844000 DOWN
ENSG00000234396 1.313836 1.513997 0.5069778 2.986318 2.823587e-03 0.0267502859 UP
ENSG00000078900 159.209635 -1.708001 0.4537402 -3.764271 1.670355e-04 0.0040623446 DOWN
ENSG00000235131 3.292931 -2.277330 0.6918335 -3.291732 9.957256e-04 0.0134204677 DOWN
ENSG00000196581 10.582909 1.822511 0.6121410 2.977273 2.908251e-03 0.0273166596 UP
ENSG00000187017 79.130853 -2.709708 0.5869882 -4.616290 3.906606e-06 0.0002934384 Low
Here the issue is the column containing the ENSG
id is now empty, which I want to assign name as gene
I can rename each file but again its a long process to rename each file individually. So how to do that before i save my list
into individual or in other words after this step
results1 <- lapply(contrasts, function(x) results(dds, contrast=x)) ## my code
My final expected output
gene baseMean log2FoldChange lfcSE stat pvalue padj UP_DOWN
1 ENSG00000237973 10550.545143 -1.626252 0.3987092 -4.078792 4.527033e-05 0.0015844000 DOWN
2 ENSG00000234396 1.313836 1.513997 0.5069778 2.986318 2.823587e-03 0.0267502859 UP
3 ENSG00000078900 159.209635 -1.708001 0.4537402 -3.764271 1.670355e-04 0.0040623446 DOWN
4 ENSG00000235131 3.292931 -2.277330 0.6918335 -3.291732 9.957256e-04 0.0134204677 DOWN
5 ENSG00000196581 10.582909 1.822511 0.6121410 2.977273 2.908251e-03 0.0273166596 UP
6 ENSG00000187017 79.130853 -2.709708 0.5869882 -4.616290 3.906606e-06 0.0002934384 Low
Any suggestion or help would be really appreciated .