I have a following list of data.tables;
l[1:2]
$cluster1
rn p_val avg_log2FC pct.1 pct.2 p_val_adj
<char> <num> <num> <num> <num> <num>
1: Adamts20 1.438101e-65 1.030705 0.001 0.118 4.314302e-62
2: Gal 3.233897e-54 16.358484 0.006 0.208 9.701690e-51
3: Hrnr 1.295286e-51 14.374645 0.007 0.182 3.885858e-48
4: Ngb 4.143060e-44 1.925631 0.021 0.240 1.242918e-40
5: Svep1 3.872262e-41 8.232291 0.283 0.582 1.161679e-37
---
366: Cyfip2 1.468792e-05 2.417948 0.056 0.118 4.406375e-02
367: Fcgr2b 1.505992e-05 -4.719973 0.231 0.148 4.517976e-02
368: Ogn 1.538930e-05 9.708295 0.242 0.339 4.616791e-02
369: Lrrc15 1.549036e-05 -2.966498 0.241 0.352 4.647109e-02
370: AY036118 1.624054e-05 2.602963 0.715 0.788 4.872162e-02
$cluster2
rn p_val avg_log2FC pct.1 pct.2 p_val_adj
<char> <num> <num> <num> <num> <num>
1: Samd13 1.841651e-127 8.7785032 0.001 0.144 5.524952e-124
2: Gata1 2.210414e-99 17.0522687 0.002 0.126 6.631242e-96
3: Col4a4 1.250827e-58 9.6145811 0.583 0.254 3.752481e-55
4: Bsx 4.028430e-54 18.2214242 0.202 0.568 1.208529e-50
5: Gimap3 4.650536e-53 -1.6106639 0.017 0.255 1.395161e-49
---
217: Cd3e 1.452524e-05 18.6983055 0.131 0.175 4.357573e-02
218: Selenom 1.455810e-05 0.9648215 0.293 0.201 4.367429e-02
219: A330069E16Rik 1.469167e-05 -5.4387846 0.388 0.282 4.407501e-02
220: Lypd1 1.560834e-05 -2.1249661 0.176 0.100 4.682501e-02
221: Alad 1.633998e-05 -1.1929284 0.226 0.175 4.901995e-02
I'd like to export this list to a csv file by fwrite. I run this following code;
lapply(l[1:2], function(x) fwrite(as.data.table(x), "DGE.csv"))
A resulting csv file doesn't have list element names, $cluster1 and $cluster. Are there any ways to add list element names as the header of each of the element list and column headers as a follow desired output by using fwrite ?;
cluster1
rn p_val avg_log2FC pct.1 pct.2 p_val_adj
Samd13 1.84E-127 8.778503219 0.001 0.144 5.52E-124
Gata1 2.21E-99 17.05226868 0.002 0.126 6.63E-96
Col4a4 1.25E-58 9.614581115 0.583 0.254 3.75E-55
Bsx 4.03E-54 18.22142419 0.202 0.568 1.21E-50
Gimap3 4.65E-53 -1.61066387 0.017 0.255 1.40E-49
Gm26825 9.54E-51 12.96067221 0.341 0.596 2.86E-47
Erfe 3.72E-48 11.74946067 0.007 0.156 1.12E-44
cluster2
rn p_val avg_log2FC pct.1 pct.2 p_val_adj
Samd13 1.63E-12 15.05539372 0.038 0.141 4.90E-09
Frmd5 1.75E-12 -1.28277874 0.154 0.318 5.26E-09
Pla2g2f 2.06E-12 -1.51234633 0.142 0.056 6.17E-09
Aldh1a2 2.25E-12 5.127605606 0.274 0.426 6.75E-09
Fxyd2 2.51E-12 5.246386986 0.626 0.805 7.53E-09
Adam30 3.15E-12 1.53746735 0.203 0.362 9.44E-09
Gpr35 3.15E-12 -3.18282304 0.691 0.516 9.46E-09
Il10rb 3.65E-12 1.473277609 0.42 0.598 1.10E-08
Gk5 3.72E-12 -14.0221264 0.177 0.074 1.12E-08
.......
An alternative to writing separate files: append the list-name as a column, then rbindlist them, write them, and when you read them then split on that column name.
Sample data:
library(data.table)
ZZ <- lapply(list(mt1=mtcars[1:3,], mt2=mtcars[4:6,]), as.data.table)
ZZ
# $mt1
# mpg cyl disp hp drat wt qsec vs am gear carb
# <num> <num> <num> <num> <num> <num> <num> <num> <num> <num> <num>
# 1: 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
# 2: 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
# 3: 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
# $mt2
# mpg cyl disp hp drat wt qsec vs am gear carb
# <num> <num> <num> <num> <num> <num> <num> <num> <num> <num> <num>
# 1: 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
# 2: 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
# 3: 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
Append, combine, write:
fwrite(rbindlist(ZZ, idcol = "name"), "~/Downloads/ZZ.csv")
The resulting file, that can be read by any vanilla CSV reader:
name,mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb
mt1,21,6,160,110,3.9,2.62,16.46,0,1,4,4
mt1,21,6,160,110,3.9,2.875,17.02,0,1,4,4
mt1,22.8,4,108,93,3.85,2.32,18.61,1,1,4,1
mt2,21.4,6,258,110,3.08,3.215,19.44,1,0,3,1
mt2,18.7,8,360,175,3.15,3.44,17.02,0,0,3,2
mt2,18.1,6,225,105,2.76,3.46,20.22,1,0,3,1
Reading it in and restoring the original object format:
ZZ2 <- fread("ZZ.csv")
ZZ2 <- lapply(split(ZZ2, ZZ2$name), function(x) x[, name := NULL])
ZZ2
# $mt1
# mpg cyl disp hp drat wt qsec vs am gear carb
# <num> <int> <int> <int> <num> <num> <num> <int> <int> <int> <int>
# 1: 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
# 2: 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
# 3: 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
# $mt2
# mpg cyl disp hp drat wt qsec vs am gear carb
# <num> <int> <int> <int> <num> <num> <num> <int> <int> <int> <int>
# 1: 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
# 2: 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
# 3: 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1