当 knitting 这个R Markdown进入HTML文件时，我收到一个奇怪的错误 . 我认为它与 dplyr 包中的某种不兼容性有关 knitr .
UPDATE: I replaced the cbind chunk with the dplyr::bind_cols command, as someone suggested below not to use cbind with dplyr. However, I now get a different, equally incomprehensible error:
library(dplyr) counts.all <- bind_cols(count.tables[["SF10281"]], count.tables[["SF10282"]])
我得到这个改变的错误（再次，只有在编织时）：
Error in eval(expr, envir, enclos) : not compatible with STRSXP Calls: <Anonymous> ... withVisible -> eval -> eval -> bind_cols -> cbind_all -> .Call
Previous error with cbind instead of dplyr::bind_cols:
单独运行块工作正常，我能够 knit 罚款，直到我添加最后一个块（使用 select 中的 select ） .
This is the error I get:
Quitting from lines 75-77 (Analysis_SF10281_SF10282_Sep29_2015.Rmd)
Error in UseMethod("select_") :
no applicable method for 'select_' applied to an object of class "NULL"
Calls: <Anonymous> ... withVisible -> eval -> eval -> <Anonymous> -> select_
This is the entire Rmd file:
将基因计数表读入单个数据帧列表（每个样本一个数据帧）：
```{r}
count.files <- list.files(pattern = "^SF[0-9]+_counts.txt$")
count.tables <- lapply(count.files, read.table, header=T, row.names=1)
names(count.tables) <- gsub("\\_counts.txt", "", count.files)
删除基因元数据列：
```java
```{r}
count.tables <- lapply(count.tables, `[`, -(1:5))
将单元格（列）重命名为短版本：
```java
```{r}
count.tables <- lapply(count.tables, function(x) {names(x) <- gsub("X.diazlab.aaron.tophat_out.SF[0-9]+.Sample_(SF[0-9]+).[0-9]+.([A-Z][0-9]+).accepted_hits.bam", "\\1-\\2", names(x)); x})
将对象保存到文件以供日后使用： `{r} saveRDS(count.tables, file="gliomaRawCounts_10281_10282_10345_10360.rds")`
使用所有4个样本（384个单元格）创建单个数据框，并写入文本文件：
```java
```{r}
counts.all <- cbind(count.tables[["SF10281"]], count.tables[["SF10282"]], count.tables[["SF10345"]], count.tables[["SF10360"]])
write.table(counts.all, file="gliomaRawCounts_10281_10282_10345_10360.txt", sep="\t", quote=F, col.names=NA)
读取元数据 . 不要将cell ID列指定为row.names，以便与dplyr兼容 .
```java
```{r}
meta <- read.delim("QC_metrics_SCell_SF10281_SF10282_SF10345_SF10360.txt", check.names = F, stringsAsFactors = F)
根据实时/死/多呼叫过滤单元格 . 排除空的，仅红色的和多细胞的孔：
```java
```{r, results='hide', message=FALSE, warning=FALSE}
library(dplyr)
meta.select <- filter(meta, grepl("^1g", `Live-dead_call`))
根据1,000个基因阈值过滤细胞：
```java
(Includes 12 'FAIL' cells)
```{r}
meta.select <- filter(meta.select, Genes_tagged > 1000)
子集计数表仅包括通过QC的单元格 .
```java
```{r}
counts.select <- dplyr::select(counts.all, one_of(meta.select$ID))
head(counts.select[,1:10])