r - Error in UseMethod("select_") : no applicable method for 'select_' applied to an object of class "NULL" -


i strange error when knitting r markdown html file. think has sort of incompatibility in dplyr package knitr.

update: replaced cbind chunk dplyr::bind_cols command, suggested below not use cbind dplyr. however, different, equally incomprehensible error:

library(dplyr) counts.all <- bind_cols(count.tables[["sf10281"]], count.tables[["sf10282"]])

the error change (again, when knitting):

error in eval(expr, envir, enclos) : not compatible strsxp calls: <anonymous> ... withvisible -> eval -> eval -> bind_cols -> cbind_all -> .call

previous error cbind instead of dplyr::bind_cols:

running chunks separately works fine, , able knit fine until added last chunk (using select dplyr).

this error get:

quitting lines 75-77 (analysis_sf10281_sf10282_sep29_2015.rmd)  error in usemethod("select_") :    no applicable method 'select_' applied object of class "null" calls: <anonymous> ... withvisible -> eval -> eval -> <anonymous> -> select_

this entire rmd file:

read-in gene count tables single list of data frames (one data frame per sample):

```{r} count.files <- list.files(pattern = "^sf[0-9]+_counts.txt$")  count.tables <- lapply(count.files, read.table, header=t, row.names=1)  names(count.tables) <- gsub("\\_counts.txt", "", count.files) ```

remove gene metadata columns:

```{r} count.tables <- lapply(count.tables, `[`, -(1:5)) ```

rename cells (columns) short version:

```{r} count.tables <- lapply(count.tables, function(x) {names(x) <- gsub("x.diazlab.aaron.tophat_out.sf[0-9]+.sample_(sf[0-9]+).[0-9]+.([a-z][0-9]+).accepted_hits.bam", "\\1-\\2", names(x)); x}) ```

save object file later: {r} saverds(count.tables, file="gliomarawcounts_10281_10282_10345_10360.rds")

make single data frame 4 samples (384 cells), , write text file:

```{r} counts.all <- cbind(count.tables[["sf10281"]], count.tables[["sf10282"]], count.tables[["sf10345"]], count.tables[["sf10360"]])  write.table(counts.all, file="gliomarawcounts_10281_10282_10345_10360.txt", sep="\t", quote=f, col.names=na) ```

read metadata. not assign cell id column row.names, compatibility dplyr.

```{r} meta <- read.delim("qc_metrics_scell_sf10281_sf10282_sf10345_sf10360.txt", check.names = f, stringsasfactors = f) ```

filter cells based on live/dead/multi calls. exclude empty, red-only, , multi-cell wells:

```{r, results='hide', message=false, warning=false} library(dplyr) meta.select <- filter(meta, grepl("^1g", `live-dead_call`)) ```

filter cells based on 1,000 gene threshold:

(includes 12 'fail' cells) ```{r} meta.select <- filter(meta.select, genes_tagged > 1000) ```

subset counts table include cells passed qc.

```{r} counts.select <- dplyr::select(counts.all, one_of(meta.select$id)) head(counts.select[,1:10]) ```


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